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stat-lab / EvalSVcallers

Evaluate the performances (precision and recall) of structural variation (SV) callers
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evaluate_SV_callers.pl skips some SVTYPE from simulation truth VCF for precision and Recall values calculation. #9

Open bioinfo89 opened 3 years ago

bioinfo89 commented 3 years ago

Hi,

I am using evaluate_SV_callers.pl script to compare the variants against a simulation truth VCF file which contains DEL, INS, DUP, SNP and complex variants. However, when I use this truth vcf for evaluation, the out only shows precision and recall values for Duplications leaving the other SV types.

Ref-DEL: 0      tinny (<= 100 bp): 0    short (<=1.0 kp): 0     middle (<= 100 kb): 0   large (> 100 kb): 0
Ref-INS: 0      short (<=1.0 kp): 0     middle (<= 100 kb): 0   large (> 100 kb): 0
Ref-DUP: 674    short (<=1.0 kp): 170   middle (<= 100 kb): 416 large (> 100 kb): 88
Ref-INV: 0      short (<=1.0 kp): 0     middle (<= 100 kb): 0   large (> 100 kb): 0

It also throws the following errors:

Use of uninitialized value $type in hash element at /home/krc190002/scratch/WGS_tools/EvalSVcallers/scripts/evaluate_SV_callers.pl line 365, <FILE> line 127.
Use of uninitialized value $type in hash element at /home/krc190002/scratch/WGS_tools/EvalSVcallers/scripts/evaluate_SV_callers.pl line 367, <FILE> line 127.
Use of uninitialized value $type in pattern match (m//) at /home/krc190002/scratch/WGS_tools/EvalSVcallers/scripts/evaluate_SV_callers.pl line 368, <FILE> line 127.
Use of uninitialized value $type in string eq at /home/krc190002/scratch/WGS_tools/EvalSVcallers/scripts/evaluate_SV_callers.pl line 369, <FILE> line 127.

Any help to resolve this would be great. Thanks!

stat-lab commented 3 years ago

Would you let me show the command used in this job? Also try to use the latest EvalSVcallers package.

bioinfo89 commented 3 years ago

Below mentioned is the command I am using:

perl EvalSVcallers/scripts/evaluate_SV_callers.pl -r2 ../Simchr21.truth.vcf chr21sim_Delly_raw_SVs_mq20_excllcr.converted.vcf -rs 2

bioinfo89 commented 3 years ago

I tried the latest EvalSVCallers package, throws the same errors.

stat-lab commented 3 years ago

Please show the first three lines (except for the headers) of your vcf file "Simchr21.truth.vcf"for the simulated reference SVs.

bioinfo89 commented 3 years ago 
chr21   9411198 nsv1132545      TN      <DUP:TANDEM>    .       PASS    VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=26001   GT:CN   1|1:2|2
chr21   9438397 nsv1146288      CN      <DUP:TANDEM>    .       PASS    VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=21802   GT:CN   0|1:1|2
chr21   9444798 nsv1132546      AN      <DUP:TANDEM>    .       PASS    VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=39001   GT:CN   1|0:2|1
stat-lab commented 3 years ago

Could you send me the Simchr21.truth.vcf file? If the file contains the lines other than DUP, do these lines have SVTYPE=DEL, SVTYPE=INS, or SVTYPE=INV at the 8th column?

2020/09/11 10:55、bioinfo89 notifications@github.comのメール:

chr21 9411198 nsv1132545 TN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=26001 GT:CN 1|1:2|2 chr21 9438397 nsv1146288 CN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=21802 GT:CN 0|1:1|2 chr21 9444798 nsv1132546 AN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=39001 GT:CN 1|0:2|1 — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-690826159, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIBV3BLTGOS4JBEID2XTT3SFF7P3ANCNFSM4RF5G6QA.

bioinfo89 commented 3 years ago

Yes. I am not able to attach the vcf file here.

bioinfo89 commented 3 years ago

Please find attached the truth VCF file. Best, Khyati Chandratre

On 10 Sep 2020, at 11:37 PM, stat-lab notifications@github.com wrote:

Could you send me the Simchr21.truth.vcf file? If the file contains the lines other than DUP, do these lines have SVTYPE=DEL, SVTYPE=INS, or SVTYPE=INV at the 8th column?

2020/09/11 10:55、bioinfo89 notifications@github.comのメール:

chr21 9411198 nsv1132545 TN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=26001 GT:CN 1|1:2|2 chr21 9438397 nsv1146288 CN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=21802 GT:CN 0|1:1|2 chr21 9444798 nsv1132546 AN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=39001 GT:CN 1|0:2|1 — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-690826159, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIBV3BLTGOS4JBEID2XTT3SFF7P3ANCNFSM4RF5G6QA.

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stat-lab commented 3 years ago

Could you sed the file to the following address? Email address: shunichi.kosugi@riken.jp mailto:shunichi.kosugi@riken.jp

2020/09/11 13:49、bioinfo89 notifications@github.comのメール:

Please find attached the truth VCF file. Best, Khyati Chandratre

On 10 Sep 2020, at 11:37 PM, stat-lab notifications@github.com wrote:

Could you send me the Simchr21.truth.vcf file? If the file contains the lines other than DUP, do these lines have SVTYPE=DEL, SVTYPE=INS, or SVTYPE=INV at the 8th column?

2020/09/11 10:55、bioinfo89 notifications@github.comのメール:

chr21 9411198 nsv1132545 TN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=26001 GT:CN 1|1:2|2 chr21 9438397 nsv1146288 CN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=21802 GT:CN 0|1:1|2 chr21 9444798 nsv1132546 AN . PASS VARIANT_OVERALL_TYPE=TandemDup;SVTYPE=DUP;SVLEN=39001 GT:CN 1|0:2|1 — You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-690826159, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIBV3BLTGOS4JBEID2XTT3SFF7P3ANCNFSM4RF5G6QA.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-690868617, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPF2O253IMD5VNE7UO6LSFGSSDANCNFSM4RF5G6QA.

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bioinfo89 commented 3 years ago

Sent!

stat-lab commented 3 years ago

In your vcf file, many lines have no 'SVTYPE' tag in the INFO field, which causes errors. Also, SV types other than DEL, DUP, INS, and INV are not considered. In addition, short SVs (< 30 bp by default) or indels, except for INSs, are not considered for evaluation. If you want to add shorter variants for the reference SVs, you can specify the minimum size with the '-rl' option.

bioinfo89 commented 3 years ago

So, this means that the SVTYPE tag needs to be there for every record so that the script will add the types accordingly for evaluation?However, SVTYPE=DEL, INS are present along with DUP and there still are no Pr and Rc values for them in the output? I don’t understand why exactly!

Also, I want to extract True positive and False positive values from the script apart from Precision and Recall, so for that If I am modifying your script,

For A size for e.g:

FPs:int(${$call_del_num{'A'}}{$read} - ${$match_del_num{'A'}}{$read}) TPs: ${$match_del_num{'A'}}{$read}

Should display what I want right?

Best, Khyati Chandratre

On 11 Sep 2020, at 9:31 PM, stat-lab notifications@github.com wrote:

In your vcf file, many lines have no 'SVTYPE' tag in the INFO field, which causes errors. Also, SV types other than DEL, DUP, INS, and INV are not considered. In addition, short SVs (< 30 bp by default) or indels, except for INSs, are not considered for evaluation. If you want to add shorter variants for the reference SVs, you can specify the minimum size with the '-rl' option.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691386787, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPFYQ6YRFIPAVQ4MM4O3SFLMQJANCNFSM4RF5G6QA.

stat-lab commented 3 years ago

In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs?

Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls).

bioinfo89 commented 3 years ago

Ok thanks!

No all the DELs are less than 30 bps.

Best, Khyati Chandratre

On 11 Sep 2020, at 10:02 PM, stat-lab notifications@github.com wrote:

In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs?

Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691391935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPF2XJGSGXBLR7R6DF53SFLQGBANCNFSM4RF5G6QA.

bioinfo89 commented 3 years ago

I am getting precision value >100% for duplications size M, for e.g. 100.2 How can it be >100%?

Best, Khyati Chandratre

On 11 Sep 2020, at 10:02 PM, stat-lab notifications@github.com wrote:

In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs?

Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691391935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPF2XJGSGXBLR7R6DF53SFLQGBANCNFSM4RF5G6QA.

stat-lab commented 3 years ago

Please send the DUP lists of size M in your test vcf and the reference vcf, respectively.

2020/09/12 12:19、bioinfo89 notifications@github.comのメール:

I am getting precision value >100% for duplications size M, for e.g. 100.2 How can it be >100%?

Best, Khyati Chandratre

On 11 Sep 2020, at 10:02 PM, stat-lab notifications@github.com wrote:

In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs?

Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691391935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPF2XJGSGXBLR7R6DF53SFLQGBANCNFSM4RF5G6QA.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691394696, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIBV3DRYJQM7WS4KOQ673LSFLSENANCNFSM4RF5G6QA.

bioinfo89 commented 3 years ago

Please find the attachments. Thanks!

Best, Khyati Chandratre

On 11 Sep 2020, at 10:54 PM, stat-lab notifications@github.com wrote:

Please send the DUP lists of size M in your test vcf and the reference vcf, respectively.

2020/09/12 12:19、bioinfo89 notifications@github.comのメール:

I am getting precision value >100% for duplications size M, for e.g. 100.2 How can it be >100%?

Best, Khyati Chandratre

On 11 Sep 2020, at 10:02 PM, stat-lab notifications@github.com wrote:

In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs?

Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691391935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPF2XJGSGXBLR7R6DF53SFLQGBANCNFSM4RF5G6QA.

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chr21 14494279 esv3438101 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26036539 nsv4290919 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15431962 nsv979524 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26330173 Novel_77 CA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34404309 esv3646901 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15814028 nsv4279442 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46882645 dgv4438n100 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30065750 Novel_78 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10391397 nsv1151813 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18539217 Novel_59 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23193886 nsv819310 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 39483259 nsv834097 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9940899 nsv953323 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29419197 nsv4533246 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29215325 nsv979529 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 39923185 Novel_274 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29584073 Novel_130 CC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38394963 esv3575389 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25993548 nsv4289927 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46542668 nsv522002 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 41289889 Novel_202 GA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9514197 nsv1147196 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40833992 nsv4277282 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 33817954 nsv962672 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38296901 nsv1160711 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45260242 nsv4276812 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15941345 esv3646433 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28333934 Novel_19 CA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 41529720 Novel_136 AG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10365997 nsv1151143 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43477263 Novel_98 GT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34921298 nsv1115615 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 35634584 nsv587420 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 41853188 nsv4283330 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 33387854 nsv1057535 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14521579 dgv2469e59 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45100454 nsv4273762 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43067927 Novel_174 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46749716 nsv520123 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43426374 nsv828882 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47974053 esv2760700 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38739899 nsv953362 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15380398 nsv1118677 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44109940 nsv4285035 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27299632 esv3575384 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14369205 nsv1160694 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36380023 Novel_376 CA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37244127 nsv1056646 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15096622 nsv962665 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34047660 esv3646891 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34737058 Novel_257 GC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28467923 Novel_37 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9681397 nsv1077393 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24602610 nsv4283816 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10697897 nsv1154052 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42827366 esv3647063 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28058520 Novel_285 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19713819 esv3893383 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28162153 Novel_21 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28189699 nsv953350 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34421894 nsv4282152 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25752242 Novel_256 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37033227 nsv1063801 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18612309 nsv828827 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21577853 nsv4285555 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23218841 esv2762097 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9530697 nsv1152790 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18706034 nsv1059387 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36995158 Novel_194 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44258769 Novel_275 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9484797 nsv1151538 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29016158 nsv4287396 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23316907 nsv4286264 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34204192 esv3646896 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23795603 nsv1060531 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19621198 nsv4273779 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23556198 nsv4278080 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34555853 Novel_80 CA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29268236 nsv4284843 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 31284342 Novel_172 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24737827 nsv4275808 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26664533 Novel_278 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14452245 esv3893362 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9503497 nsv1150699 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43834198 nsv4274948 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19610934 Novel_358 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40981638 esv27418 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16382146 nsv517307 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45019897 nsv1147937 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30974170 Novel_153 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34659999 nsv587378 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43276781 nsv522791 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16673849 Novel_67 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 33867159 esv3646885 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10094698 nsv1128843 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46848587 nsv587847 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 31173528 Novel_320 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 22143527 nsv587206 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45205978 nsv4280670 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29241966 Novel_9 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15064677 nsv965996 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27894245 nsv4273932 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37857725 nsv4286971 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47051722 esv3405686 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30842516 nsv4282313 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10122297 nsv1145813 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37857574 esv3646973 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46243229 nsv4283081 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38831527 nsv4274417 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21659198 nsv4284470 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29370239 Novel_63 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 35383198 dgv1517n166 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36041688 Novel_225 GG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47060198 nsv4277334 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9935099 nsv953322 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46117310 nsv1120413 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17885267 nsv4287610 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9697297 nsv1147025 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37879841 Novel_220 CC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14488324 nsv979549 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 22250697 nsv4281251 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24483291 nsv470891 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26464271 nsv1064254 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 33859817 Novel_377 CA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15081288 nsv979522 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20620456 Novel_276 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32408552 Novel_332 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20641368 nsv1063259 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46085479 nsv4287311 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 39084799 Novel_162 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43677829 nsv459273 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32591329 nsv4289599 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43134928 Novel_151 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9702998 nsv1128838 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26040740 nsv470895 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15615218 nsv520538 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23438820 nsv4289734 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45039443 esv3647110 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36258023 nsv587431 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20956911 nsv1061476 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15039842 nsv965994 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42782629 esv3893413 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40103879 dgv4431n100 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44061666 esv3647086 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19323718 nsv587088 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15089305 nsv9850 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17057042 nsv1060139 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27291697 nsv1146320 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36031697 nsv1154148 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10084898 nsv1132553 NN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16924719 Novel_142 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32842805 nsv4286067 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 41867194 dgv4434n100 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20992179 esv3331936 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15762761 Novel_140 AT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40053563 nsv4287688 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38342066 Novel_165 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34694266 nsv587387 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19448307 Novel_38 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25732439 Novel_235 AT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10697895 dgv2455e59 NN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17851451 nsv4286286 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14371697 nsv1077921 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38313400 nsv4288817 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9444798 nsv1132546 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 31435410 nsv4280280 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 22158608 nsv526431 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23326808 Novel_96 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25553210 dgv530n27 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9737698 nsv4292235 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34477202 Novel_237 AG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37782212 nsv1064194 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42726273 esv3647061 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20667993 nsv4279259 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44983476 nsv965984 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16588270 nsv819831 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37928997 nsv962676 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14504453 Novel_22 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15933067 Novel_300 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37174799 nsv953358 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23084860 nsv4274030 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36485088 nsv4275555 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34644080 nsv587376 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17857576 nsv4282367 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9524198 nsv1139766 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46341252 esv3575398 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47608578 nsv1062031 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 22053154 nsv4279875 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23084709 esv3646584 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19280003 nsv4278589 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 33250495 nsv4537168 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45235398 nsv1124846 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43759076 Novel_141 AG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37812708 Novel_324 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27141170 nsv965977 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9645597 nsv1077392 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 35383914 esv24747 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26642657 Novel_102 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19664797 nsv1077922 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40940198 nsv4277363 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27051133 nsv4273442 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14338197 nsv1078498 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37963482 Novel_311 GG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47542777 dgv255n21 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28216064 nsv528278 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18772528 nsv1129674 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36297661 esv3646930 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25933597 nsv1078501 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10861022 nsv962657 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14412397 nsv1078499 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36277299 nsv953357 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45322429 Novel_143 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32662698 nsv4272638 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 48101804 nsv979560 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36051245 Novel_177 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20446198 nsv4289316 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14338453 esv29704 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24728593 esv3646650 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20264109 nsv4279276 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17251598 nsv1132560 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30723570 nsv4282026 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25881449 nsv4280765 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43177638 nsv4285100 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 48055718 nsv9864 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 39846569 nsv1064436 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 39335432 nsv1060057 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20053157 esv2763677 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19125389 Novel_66 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21552598 Novel_97 AT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15894599 nsv953341 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40555799 nsv953626 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21504675 Novel_294 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36092360 Novel_10 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25067674 Novel_70 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46240230 Novel_232 GC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42446436 Novel_155 GA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14454520 nsv3360048 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18665494 nsv4284908 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47836120 nsv819608 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9708097 nsv1151438 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17285389 nsv4288816 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16328777 Novel_1 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9411198 nsv1132545 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17350441 Novel_166 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15033179 esv3426562 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32360407 Novel_262 CC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44247271 nsv4278168 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17497491 Novel_205 GT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 22223994 nsv4285080 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18503517 Novel_39 CC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15392093 nsv965973 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21388594 nsv4280168 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46194746 Novel_323 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30112975 Novel_239 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38486397 nsv1152243 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29793256 Novel_168 AT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21816277 nsv1160701 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20230063 nsv965974 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 31123409 nsv4273624 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34694159 dgv7817n54 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10186398 nsv1110378 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23556169 nsv1111224 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26733644 nsv964489 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34783173 nsv965982 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16068671 nsv4289283 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 31639081 Novel_13 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34360643 Novel_164 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34180845 Novel_335 GT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47712422 dgv2516e59 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40714341 nsv979537 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42729835 nsv528279 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40456134 Novel_340 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34293158 Novel_125 GT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18268198 nsv4277325 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19360065 esv3646490 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 41275616 nsv4289800 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9438397 nsv1146288 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40345402 Novel_57 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 35939411 nsv518782 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28791995 nsv965980 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32741106 nsv587363 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26578836 nsv4279770 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30562998 nsv4276289 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47679408 Novel_99 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16156198 nsv4286393 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14518079 esv3383309 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43712481 dgv2497e59 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45023822 esv3449507 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10100697 nsv1146200 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18029885 esv3646464 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37387523 nsv964494 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25822972 nsv522112 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9502898 nsv1139765 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28413703 Novel_82 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38345141 Novel_352 AT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10366098 nsv1124841 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9689997 nsv1150181 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18306491 Novel_20 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34517182 Novel_328 AG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42364480 dgv2495e59 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 31406780 Novel_230 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 35528078 Novel_198 GA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26024480 nsv518444 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16652671 Novel_5 GT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16532434 Novel_319 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21005579 esv3401444 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38160027 nsv4288882 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47589097 dgv7922n54 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37002141 Novel_79 TG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37839588 nsv4288000 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40675940 nsv4274342 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43010100 nsv4288610 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27542344 Novel_355 GA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21407282 Novel_315 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42384180 esv3375500 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47165322 dgv2512e59 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46851487 Novel_107 CC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9485298 nsv1124838 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21769745 nsv4288786 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 22199464 nsv964487 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16521611 nsv4278276 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40668784 nsv962678 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19504736 esv2763238 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47612397 nsv1148428 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20564444 Novel_312 GT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15029779 esv3333900 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24970036 Novel_88 AT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37922875 esv28981 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 35416864 nsv4285331 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32782048 nsv4274900 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24414293 nsv1060249 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28282658 nsv1067026 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 25968986 Novel_106 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43603181 dgv2496e59 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 29926798 Novel_267 TA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24650078 esv3646646 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36973799 nsv4536893 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 31322817 esv3646814 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15538482 esv3575380 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30982438 nsv4290072 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20047358 nsv828830 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37185128 esv3646951 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23019989 nsv828839 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19155399 nsv953347 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 21733705 nsv4284784 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23576203 nsv4282205 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23531720 Novel_310 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 36458335 Novel_15 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37911380 esv3384461 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43830581 dgv2498e59 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46321422 esv3347085 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 42274249 Novel_53 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20436613 nsv828832 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15401598 nsv979523 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 26084867 nsv4276616 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 18486294 nsv4273294 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27089202 nsv4290541 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 48105198 nsv1139773 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15405799 nsv964484 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46080919 nsv1111232 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32801019 nsv4282987 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27606395 nsv965978 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34768785 esv3646904 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23307641 nsv4283053 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47025997 nsv1077402 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44054898 nsv1115616 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15054705 nsv965995 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45031624 esv3647109 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17762949 nsv4288319 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 34847198 nsv4292022 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27551895 esv3646729 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 33800491 nsv962671 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 22320874 nsv520445 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47046927 Novel_284 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 37404265 nsv587463 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 24596242 nsv4292201 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 19306198 nsv4274758 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 14510920 nsv3369501 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46920165 esv3326161 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45155218 esv33771 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17474601 Novel_84 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 32031154 Novel_158 TC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30585679 esv3432441 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 38195785 Novel_271 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43374481 esv3347434 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44140692 esv3575391 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 11176202 nsv962660 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20692299 Novel_325 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 45027524 Novel_122 CT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10174498 nsv1110377 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 15456263 esv32571 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 43790548 nsv4282448 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44963684 nsv587691 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 48108198 nsv4281445 CN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 33985037 nsv979533 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 10990897 nsv1148217 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46240264 nsv4283413 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 48062198 nsv4284099 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17984298 nsv4289926 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 30594758 nsv979531 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16470471 Novel_46 GT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 27451083 nsv4292016 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 28013250 Novel_29 TT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 39907022 Novel_321 GC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 16398597 Novel_18 AT . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47728148 nsv4284909 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 35512663 nsv4285386 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 40733021 Novel_93 AC . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 44355255 nsv4289648 AN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 23124213 Novel_224 AA . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 20510431 esv3646511 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47657594 dgv7927n54 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 17000618 nsv817914 GN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46872297 nsv1146077 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 46572620 Novel_26 AG . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 47591198 nsv4288219 TN . PASS VARIANT_OVERALL_TYPE=TandemDup SVTYPE=DUP chr21 9411199 DUP . . . PASS SVTYPE DUP SVLEN 26001 READS 44 GT 0/1 chr21 9438399 DUP . . . PASS SVTYPE DUP SVLEN 21802 READS 25 GT 0/1 chr21 9444800 DUP . . . PASS SVTYPE DUP SVLEN 39001 READS 22 GT 0/1 chr21 9484798 DUP . . . PASS SVTYPE DUP SVLEN 6402 READS 25 GT 0/1 chr21 9485300 DUP . . . PASS SVTYPE DUP SVLEN 16801 READS 24 GT 0/1 chr21 9502900 DUP . . . PASS SVTYPE DUP SVLEN 20301 READS 20 GT 0/1 chr21 9503499 DUP . . . PASS SVTYPE DUP SVLEN 5902 READS 21 GT 0/1 chr21 9514198 DUP . . . PASS SVTYPE DUP SVLEN 9002 READS 26 GT 0/1 chr21 9524200 DUP . . . PASS SVTYPE DUP SVLEN 3501 READS 21 GT 0/1 chr21 9530698 DUP . . . PASS SVTYPE DUP SVLEN 64802 READS 48 GT 0/1 chr21 9645599 DUP . . . PASS SVTYPE DUP SVLEN 33302 READS 28 GT 0/1 chr21 9689999 DUP . . . PASS SVTYPE DUP SVLEN 1903 READS 21 GT 0/1 chr21 9697298 DUP . . . PASS SVTYPE DUP SVLEN 4904 READS 17 GT 0/1 chr21 9703007 DUP . . . PASS SVTYPE DUP SVLEN 4544 READS 5 GT 0/1 chr21 9708099 DUP . . . PASS SVTYPE DUP SVLEN 26302 READS 45 GT 0/1 chr21 9737699 DUP . . . PASS SVTYPE DUP SVLEN 37738 READS 44 GT 0/1 chr21 9935101 DUP . . . PASS SVTYPE DUP SVLEN 5002 READS 6 GT 0/1 chr21 9940901 DUP . . . PASS SVTYPE DUP SVLEN 93800 READS 12 GT 0/1 chr21 10084949 DUP . . . PASS SVTYPE DUP SVLEN 4239 READS 16 GT 0/1 chr21 10094700 DUP . . . PASS SVTYPE DUP SVLEN 5501 READS 21 GT 0/1 chr21 10100699 DUP . . . PASS SVTYPE DUP SVLEN 20902 READS 18 GT 0/1 chr21 10122322 DUP . . . LowQual SVTYPE DUP SVLEN 51324 READS 2 GT 0/1 chr21 10174557 DUP . . . PASS SVTYPE DUP SVLEN 11645 READS 9 GT 0/1 chr21 10186400 DUP . . . PASS SVTYPE DUP SVLEN 23403 READS 16 GT 0/1 chr21 10365999 DUP . . . PASS SVTYPE DUP SVLEN 8502 READS 16 GT 0/1 chr21 10366095 DUP . . . PASS SVTYPE DUP SVLEN 19301 READS 31 GT 0/1 chr21 10391399 DUP . . . PASS SVTYPE DUP SVLEN 96502 READS 51 GT 0/1 chr21 10697897 DUP . . . PASS SVTYPE DUP SVLEN 39983 READS 28 GT 0/1 chr21 10698016 DUP . . . PASS SVTYPE DUP SVLEN 72053 READS 9 GT 0/1 chr21 10861024 DUP . . . PASS SVTYPE DUP SVLEN 3167 READS 218 GT 0/1 chr21 10990899 DUP . . . PASS SVTYPE DUP SVLEN 11202 READS 24 GT 0/1 chr21 11176204 DUP . . . PASS SVTYPE DUP SVLEN 11926 READS 231 GT 0/1 chr21 14338198 DUP . . . PASS SVTYPE DUP SVLEN 32587 READS 13 GT 0/1 chr21 14338455 DUP . . . PASS SVTYPE DUP SVLEN 30170 READS 49 GT 0/1 chr21 14369207 DUP . . . PASS SVTYPE DUP SVLEN 77506 READS 15 GT 0/1 chr21 14371729 DUP . . . PASS SVTYPE DUP SVLEN 39573 READS 19 GT 0/1 chr21 14412399 DUP . . . PASS SVTYPE DUP SVLEN 31302 READS 18 GT 0/1 chr21 14452247 DUP . . . PASS SVTYPE DUP SVLEN 59082 READS 704 GT 0/1 chr21 14454521 DUP . . . PASS SVTYPE DUP SVLEN 27200 READS 109 GT 0/1 chr21 14488326 DUP . . . PASS SVTYPE DUP SVLEN 4816 READS 227 GT 0/1 chr21 14494281 DUP . . . PASS SVTYPE DUP SVLEN 9999 READS 25 GT 0/0 chr21 14504454 DUP . . . PASS SVTYPE DUP SVLEN 3604 READS 17 GT 0/0 chr21 14510922 DUP . . . PASS SVTYPE DUP SVLEN 12200 READS 74 GT 0/1 chr21 14518080 DUP . . . PASS SVTYPE DUP SVLEN 2101 READS 18 GT 0/1 chr21 14521581 DUP . . . PASS SVTYPE DUP SVLEN 8199 READS 45 GT 0/1 chr21 15029780 DUP . . . PASS SVTYPE DUP SVLEN 1599 READS 24 GT 0/1 chr21 15033180 DUP . . . PASS SVTYPE DUP SVLEN 2599 READS 30 GT 0/1 chr21 15039844 DUP . . . PASS SVTYPE DUP SVLEN 4400 READS 210 GT 0/1 chr21 15054707 DUP . . . PASS SVTYPE DUP SVLEN 1295 READS 203 GT 0/1 chr21 15064678 DUP . . . PASS SVTYPE DUP SVLEN 5269 READS 243 GT 0/1 chr21 15081290 DUP . . . PASS SVTYPE DUP SVLEN 4705 READS 217 GT 0/1 chr21 15089307 DUP . . . PASS SVTYPE DUP SVLEN 4325 READS 52 GT 0/1 chr21 15096623 DUP . . . PASS SVTYPE DUP SVLEN 76618 READS 281 GT 0/1 chr21 15380400 DUP . . . PASS SVTYPE DUP SVLEN 8001 READS 44 GT 0/1 chr21 15392093 DUP . . . PASS SVTYPE DUP SVLEN 2498 READS 434 GT 0/1 chr21 15401600 DUP . . . PASS SVTYPE DUP SVLEN 1382 READS 239 GT 0/1 chr21 15405799 DUP . . . PASS SVTYPE DUP SVLEN 1336 READS 204 GT 0/1 chr21 15456264 DUP . . . PASS SVTYPE DUP SVLEN 11690 READS 23 GT 0/1 chr21 15538484 DUP . . . PASS SVTYPE DUP SVLEN 14607 READS 18 GT 0/1 chr21 15615220 DUP . . . PASS SVTYPE DUP SVLEN 45320 READS 61 GT 0/1 chr21 15762762 DUP . . . PASS SVTYPE DUP SVLEN 41664 READS 67 GT 0/1 chr21 15814030 DUP . . . PASS SVTYPE DUP SVLEN 9745 READS 21 GT 0/1 chr21 15894601 DUP . . . PASS SVTYPE DUP SVLEN 28200 READS 19 GT 0/1 chr21 15933069 DUP . . . PASS SVTYPE DUP SVLEN 3602 READS 50 GT 0/1 chr21 15941347 DUP . . . PASS SVTYPE DUP SVLEN 88052 READS 24 GT 0/1 chr21 16068670 DUP . . . PASS SVTYPE DUP SVLEN 2316 READS 12 GT 0/1 chr21 16156198 DUP . . . PASS SVTYPE DUP SVLEN 21003 READS 13 GT 0/1 chr21 16328779 DUP . . . PASS SVTYPE DUP SVLEN 26202 READS 20 GT 0/1 chr21 16382148 DUP . . . PASS SVTYPE DUP SVLEN 5756 READS 127 GT 0/1 chr21 16398598 DUP . . . PASS SVTYPE DUP SVLEN 10701 READS 23 GT 0/1 chr21 16470472 DUP . . . PASS SVTYPE DUP SVLEN 10902 READS 31 GT 0/1 chr21 16521613 DUP . . . PASS SVTYPE DUP SVLEN 1625 READS 47 GT 0/1 chr21 16532436 DUP . . . PASS SVTYPE DUP SVLEN 1799 READS 45 GT 0/1 chr21 16588272 DUP . . . PASS SVTYPE DUP SVLEN 3642 READS 17 GT 0/1 chr21 16652673 DUP . . . PASS SVTYPE DUP SVLEN 1801 READS 21 GT 0/1 chr21 16673851 DUP . . . PASS SVTYPE DUP SVLEN 56400 READS 26 GT 0/1 chr21 16924721 DUP . . . PASS SVTYPE DUP SVLEN 42291 READS 71 GT 0/1 chr21 17000620 DUP . . . PASS SVTYPE DUP SVLEN 10160 READS 28 GT 0/1 chr21 17057043 DUP . . . PASS SVTYPE DUP SVLEN 43232 READS 19 GT 0/1 chr21 17251600 DUP . . . PASS SVTYPE DUP SVLEN 3001 READS 20 GT 0/1 chr21 17285391 DUP . . . PASS SVTYPE DUP SVLEN 26286 READS 15 GT 0/1 chr21 17350443 DUP . . . PASS SVTYPE DUP SVLEN 2602 READS 23 GT 0/1 chr21 17474603 DUP . . . PASS SVTYPE DUP SVLEN 12001 READS 32 GT 0/1 chr21 17497492 DUP . . . PASS SVTYPE DUP SVLEN 25329 READS 33 GT 0/1 chr21 17762950 DUP . . . PASS SVTYPE DUP SVLEN 12854 READS 10 GT 0/1 chr21 17851453 DUP . . . PASS SVTYPE DUP SVLEN 3982 READS 43 GT 0/1 chr21 17857578 DUP . . . PASS SVTYPE DUP SVLEN 3553 READS 35 GT 0/1 chr21 17885269 DUP . . . PASS SVTYPE DUP SVLEN 49786 READS 18 GT 0/1 chr21 17984300 DUP . . . PASS SVTYPE DUP SVLEN 10967 READS 38 GT 0/1 chr21 18029887 DUP . . . PASS SVTYPE DUP SVLEN 20801 READS 48 GT 0/1 chr21 18268199 DUP . . . PASS SVTYPE DUP SVLEN 22001 READS 23 GT 0/1 chr21 18306493 DUP . . . PASS SVTYPE DUP SVLEN 1902 READS 20 GT 0/1 chr21 18486296 DUP . . . PASS SVTYPE DUP SVLEN 13698 READS 42 GT 0/1 chr21 18503518 DUP . . . PASS SVTYPE DUP SVLEN 2499 READS 31 GT 0/1 chr21 18539255 DUP . . . PASS SVTYPE DUP SVLEN 9506 READS 282 GT 0/1 chr21 18612311 DUP . . . PASS SVTYPE DUP SVLEN 6675 READS 17 GT 0/1 chr21 18665496 DUP . . . PASS SVTYPE DUP SVLEN 2701 READS 20 GT 0/1 chr21 18706036 DUP . . . PASS SVTYPE DUP SVLEN 64793 READS 43 GT 0/1 chr21 18772455 DUP . . . PASS SVTYPE DUP SVLEN 32446 READS 26 GT 0/1 chr21 19125391 DUP . . . PASS SVTYPE DUP SVLEN 28600 READS 87 GT 0/1 chr21 19155401 DUP . . . PASS SVTYPE DUP SVLEN 14200 READS 43 GT 0/1 chr21 19279980 DUP . . . PASS SVTYPE DUP SVLEN 3503 READS 17 GT 0/1 chr21 19306199 DUP . . . PASS SVTYPE DUP SVLEN 12201 READS 20 GT 0/1 chr21 19323719 DUP . . . PASS SVTYPE DUP SVLEN 4341 READS 24 GT 0/1 chr21 19360065 DUP . . . PASS SVTYPE DUP SVLEN 21938 READS 15 GT 0/1 chr21 19448305 DUP . . . PASS SVTYPE DUP SVLEN 40170 READS 37 GT 0/1 chr21 19504735 DUP . . . PASS SVTYPE DUP SVLEN 16239 READS 24 GT 0/1 chr21 19610936 DUP . . . PASS SVTYPE DUP SVLEN 5862 READS 27 GT 0/1 chr21 19621200 DUP . . . PASS SVTYPE DUP SVLEN 6001 READS 40 GT 0/1 chr21 19664798 DUP . . . PASS SVTYPE DUP SVLEN 3302 READS 49 GT 0/1 chr21 19713821 DUP . . . PASS SVTYPE DUP SVLEN 70072 READS 30 GT 0/1 chr21 20047360 DUP . . . PASS SVTYPE DUP SVLEN 1438 READS 36 GT 0/1 chr21 20053159 DUP . . . PASS SVTYPE DUP SVLEN 28717 READS 520 GT 1/1 chr21 20230065 DUP . . . PASS SVTYPE DUP SVLEN 2369 READS 222 GT 0/1 chr21 20264111 DUP . . . PASS SVTYPE DUP SVLEN 30020 READS 20 GT 0/1 chr21 20436614 DUP . . . PASS SVTYPE DUP SVLEN 1391 READS 16 GT 0/1 chr21 20446199 DUP . . . PASS SVTYPE DUP SVLEN 30201 READS 15 GT 0/1 chr21 20510432 DUP . . . PASS SVTYPE DUP SVLEN 10472 READS 17 GT 0/1 chr21 20564446 DUP . . . PASS SVTYPE DUP SVLEN 16001 READS 26 GT 0/1 chr21 20620458 DUP . . . PASS SVTYPE DUP SVLEN 47006 READS 21 GT 0/1 chr21 20641370 DUP . . . PASS SVTYPE DUP SVLEN 46856 READS 22 GT 0/1 chr21 20667995 DUP . . . PASS SVTYPE DUP SVLEN 36718 READS 25 GT 0/1 chr21 20692301 DUP . . . PASS SVTYPE DUP SVLEN 1192 READS 30 GT 0/1 chr21 20956911 DUP . . . PASS SVTYPE DUP SVLEN 44007 READS 17 GT 0/1 chr21 20992181 DUP . . . PASS SVTYPE DUP SVLEN 4199 READS 28 GT 0/1 chr21 21005580 DUP . . . PASS SVTYPE DUP SVLEN 1799 READS 23 GT 0/1 chr21 21388595 DUP . . . PASS SVTYPE DUP SVLEN 2442 READS 21 GT 0/1 chr21 21407284 DUP . . . PASS SVTYPE DUP SVLEN 1699 READS 51 GT 0/1 chr21 21504676 DUP . . . PASS SVTYPE DUP SVLEN 2811 READS 22 GT 0/1 chr21 21552600 DUP . . . PASS SVTYPE DUP SVLEN 28587 READS 131 GT 0/1 chr21 21577855 DUP . . . PASS SVTYPE DUP SVLEN 6638 READS 22 GT 0/1 chr21 21659200 DUP . . . PASS SVTYPE DUP SVLEN 5001 READS 21 GT 0/1 chr21 21733707 DUP . . . PASS SVTYPE DUP SVLEN 14114 READS 51 GT 0/1 chr21 21769746 DUP . . . PASS SVTYPE DUP SVLEN 16666 READS 19 GT 0/1 chr21 21816279 DUP . . . PASS SVTYPE DUP SVLEN 2385 READS 51 GT 0/1 chr21 22053156 DUP . . . PASS SVTYPE DUP SVLEN 34633 READS 58 GT 0/1 chr21 22143529 DUP . . . PASS SVTYPE DUP SVLEN 53545 READS 25 GT 0/1 chr21 22158610 DUP . . . PASS SVTYPE DUP SVLEN 38464 READS 24 GT 0/1 chr21 22199464 DUP . . . PASS SVTYPE DUP SVLEN 1653 READS 204 GT 0/1 chr21 22223995 DUP . . . PASS SVTYPE DUP SVLEN 25185 READS 38 GT 0/1 chr21 22250699 DUP . . . PASS SVTYPE DUP SVLEN 47783 READS 47 GT 0/1 chr21 22320876 DUP . . . PASS SVTYPE DUP SVLEN 1253 READS 21 GT 0/1 chr21 23019990 DUP . . . PASS SVTYPE DUP SVLEN 1421 READS 16 GT 0/1 chr21 23084711 DUP . . . PASS SVTYPE DUP SVLEN 3531 READS 152 GT 0/1 chr21 23084862 DUP . . . PASS SVTYPE DUP SVLEN 3590 READS 0 GT 0/1 chr21 23124214 DUP . . . PASS SVTYPE DUP SVLEN 1051 READS 22 GT 0/1 chr21 23193888 DUP . . . PASS SVTYPE DUP SVLEN 9472 READS 45 GT 0/1 chr21 23218842 DUP . . . PASS SVTYPE DUP SVLEN 66306 READS 50 GT 0/1 chr21 23307643 DUP . . . PASS SVTYPE DUP SVLEN 13034 READS 26 GT 0/1 chr21 23316932 DUP . . . PASS SVTYPE DUP SVLEN 6358 READS 19 GT 0/1 chr21 23326808 DUP . . . PASS SVTYPE DUP SVLEN 38324 READS 171 GT 0/1 chr21 23438822 DUP . . . PASS SVTYPE DUP SVLEN 4516 READS 37 GT 0/1 chr21 23531722 DUP . . . PASS SVTYPE DUP SVLEN 14026 READS 113 GT 0/1 chr21 23556190 DUP . . . PASS SVTYPE DUP SVLEN 23382 READS 26 GT 0/1 chr21 23556242 DUP . . . PASS SVTYPE DUP SVLEN 5960 READS 15 GT 0/1 chr21 23576204 DUP . . . PASS SVTYPE DUP SVLEN 1410 READS 22 GT 0/1 chr21 23795605 DUP . . . PASS SVTYPE DUP SVLEN 60769 READS 20 GT 0/1 chr21 24414295 DUP . . . PASS SVTYPE DUP SVLEN 15636 READS 23 GT 0/1 chr21 24483293 DUP . . . PASS SVTYPE DUP SVLEN 47749 READS 28 GT 0/1 chr21 24596244 DUP . . . PASS SVTYPE DUP SVLEN 12359 READS 26 GT 0/1 chr21 24602611 DUP . . . PASS SVTYPE DUP SVLEN 7382 READS 23 GT 0/1 chr21 24650080 DUP . . . PASS SVTYPE DUP SVLEN 14910 READS 17 GT 0/1 chr21 24728594 DUP . . . PASS SVTYPE DUP SVLEN 3010 READS 140 GT 0/1 chr21 24737829 DUP . . . PASS SVTYPE DUP SVLEN 59369 READS 54 GT 0/1 chr21 24970038 DUP . . . PASS SVTYPE DUP SVLEN 1599 READS 26 GT 0/1 chr21 25067676 DUP . . . PASS SVTYPE DUP SVLEN 2802 READS 23 GT 0/1 chr21 25553212 DUP . . . PASS SVTYPE DUP SVLEN 38141 READS 67 GT 0/1 chr21 25732440 DUP . . . PASS SVTYPE DUP SVLEN 4002 READS 24 GT 0/1 chr21 25752244 DUP . . . PASS SVTYPE DUP SVLEN 6781 READS 53 GT 0/1 chr21 25822973 DUP . . . PASS SVTYPE DUP SVLEN 20573 READS 17 GT 0/1 chr21 25881451 DUP . . . PASS SVTYPE DUP SVLEN 2927 READS 33 GT 0/1 chr21 25933597 DUP . . . PASS SVTYPE DUP SVLEN 3202 READS 34 GT 0/1 chr21 25968988 DUP . . . PASS SVTYPE DUP SVLEN 15331 READS 446 GT 0/1 chr21 25993547 DUP . . . PASS SVTYPE DUP SVLEN 9105 READS 44 GT 0/1 chr21 26024482 DUP . . . PASS SVTYPE DUP SVLEN 1815 READS 57 GT 0/1 chr21 26036541 DUP . . . PASS SVTYPE DUP SVLEN 9984 READS 20 GT 0/1 chr21 26040742 DUP . . . PASS SVTYPE DUP SVLEN 45950 READS 19 GT 0/1 chr21 26084869 DUP . . . PASS SVTYPE DUP SVLEN 13811 READS 24 GT 0/1 chr21 26330175 DUP . . . PASS SVTYPE DUP SVLEN 9839 READS 224 GT 0/1 chr21 26464273 DUP . . . PASS SVTYPE DUP SVLEN 47406 READS 16 GT 0/1 chr21 26578838 DUP . . . PASS SVTYPE DUP SVLEN 2130 READS 20 GT 0/1 chr21 26642659 DUP . . . PASS SVTYPE DUP SVLEN 3307 READS 210 GT 0/1 chr21 26664534 DUP . . . PASS SVTYPE DUP SVLEN 59291 READS 40 GT 0/1 chr21 26733646 DUP . . . PASS SVTYPE DUP SVLEN 2329 READS 425 GT 1/1 chr21 27051135 DUP . . . PASS SVTYPE DUP SVLEN 3293 READS 32 GT 0/1 chr21 27089204 DUP . . . PASS SVTYPE DUP SVLEN 13555 READS 21 GT 0/1 chr21 27141172 DUP . . . PASS SVTYPE DUP SVLEN 3355 READS 252 GT 0/1 chr21 27299634 DUP . . . PASS SVTYPE DUP SVLEN 7786 READS 24 GT 0/1 chr21 27451084 DUP . . . PASS SVTYPE DUP SVLEN 10819 READS 15 GT 0/1 chr21 27542346 DUP . . . PASS SVTYPE DUP SVLEN 1702 READS 18 GT 0/1 chr21 27551897 DUP . . . PASS SVTYPE DUP SVLEN 12620 READS 39 GT 0/1 chr21 27606397 DUP . . . PASS SVTYPE DUP SVLEN 1317 READS 228 GT 0/1 chr21 27894247 DUP . . . PASS SVTYPE DUP SVLEN 52492 READS 25 GT 0/1 chr21 28013252 DUP . . . PASS SVTYPE DUP SVLEN 10766 READS 29 GT 0/1 chr21 28058522 DUP . . . PASS SVTYPE DUP SVLEN 70846 READS 60 GT 0/1 chr21 28162155 DUP . . . PASS SVTYPE DUP SVLEN 7002 READS 22 GT 0/1 chr21 28189701 DUP . . . PASS SVTYPE DUP SVLEN 7000 READS 51 GT 0/1 chr21 28216066 DUP . . . PASS SVTYPE DUP SVLEN 3242 READS 15 GT 0/1 chr21 28282658 DUP . . . PASS SVTYPE DUP SVLEN 15390 READS 21 GT 0/1 chr21 28333936 DUP . . . PASS SVTYPE DUP SVLEN 87603 READS 25 GT 0/1 chr21 28413705 DUP . . . PASS SVTYPE DUP SVLEN 20000 READS 261 GT 0/1 chr21 28467925 DUP . . . PASS SVTYPE DUP SVLEN 7499 READS 20 GT 0/1 chr21 28791997 DUP . . . PASS SVTYPE DUP SVLEN 2141 READS 240 GT 0/1 chr21 29016160 DUP . . . PASS SVTYPE DUP SVLEN 6328 READS 28 GT 0/1 chr21 29215327 DUP . . . PASS SVTYPE DUP SVLEN 9283 READS 219 GT 0/1 chr21 29241967 DUP . . . PASS SVTYPE DUP SVLEN 5177 READS 7 GT 0/0 chr21 29268285 DUP . . . PASS SVTYPE DUP SVLEN 59839 READS 20 GT 0/1 chr21 29370241 DUP . . . PASS SVTYPE DUP SVLEN 5001 READS 11 GT 0/1 chr21 29419198 DUP . . . PASS SVTYPE DUP SVLEN 93004 READS 19 GT 0/1 chr21 29584075 DUP . . . PASS SVTYPE DUP SVLEN 9174 READS 22 GT 0/1 chr21 29793258 DUP . . . PASS SVTYPE DUP SVLEN 23928 READS 21 GT 0/1 chr21 29926799 DUP . . . PASS SVTYPE DUP SVLEN 14981 READS 27 GT 0/1 chr21 30065752 DUP . . . PASS SVTYPE DUP SVLEN 9702 READS 23 GT 0/1 chr21 30112976 DUP . . . PASS SVTYPE DUP SVLEN 24036 READS 48 GT 0/1 chr21 30563000 DUP . . . PASS SVTYPE DUP SVLEN 21201 READS 16 GT 0/1 chr21 30585681 DUP . . . PASS SVTYPE DUP SVLEN 1199 READS 18 GT 0/1 chr21 30594759 DUP . . . PASS SVTYPE DUP SVLEN 1094 READS 414 GT 0/1 chr21 30723572 DUP . . . PASS SVTYPE DUP SVLEN 29763 READS 19 GT 0/1 chr21 30842518 DUP . . . PASS SVTYPE DUP SVLEN 51730 READS 26 GT 0/1 chr21 30974172 DUP . . . PASS SVTYPE DUP SVLEN 5701 READS 22 GT 0/1 chr21 30982440 DUP . . . PASS SVTYPE DUP SVLEN 14499 READS 21 GT 0/1 chr21 31123411 DUP . . . PASS SVTYPE DUP SVLEN 2346 READS 16 GT 0/1 chr21 31173530 DUP . . . PASS SVTYPE DUP SVLEN 54248 READS 32 GT 0/1 chr21 31284344 DUP . . . PASS SVTYPE DUP SVLEN 59712 READS 48 GT 0/1 chr21 31322818 DUP . . . PASS SVTYPE DUP SVLEN 14712 READS 20 GT 0/1 chr21 31406782 DUP . . . PASS SVTYPE DUP SVLEN 18679 READS 29 GT 0/1 chr21 31435412 DUP . . . PASS SVTYPE DUP SVLEN 38984 READS 24 GT 0/1 chr21 31639082 DUP . . . PASS SVTYPE DUP SVLEN 2302 READS 22 GT 0/1 chr21 32031156 DUP . . . PASS SVTYPE DUP SVLEN 12000 READS 23 GT 0/1 chr21 32360409 DUP . . . PASS SVTYPE DUP SVLEN 25760 READS 25 GT 0/1 chr21 32408554 DUP . . . PASS SVTYPE DUP SVLEN 47001 READS 24 GT 0/1 chr21 32591331 DUP . . . PASS SVTYPE DUP SVLEN 46251 READS 21 GT 0/1 chr21 32662699 DUP . . . PASS SVTYPE DUP SVLEN 30395 READS 20 GT 0/1 chr21 32741107 DUP . . . PASS SVTYPE DUP SVLEN 21303 READS 27 GT 0/1 chr21 32782050 DUP . . . PASS SVTYPE DUP SVLEN 15727 READS 22 GT 0/1 chr21 32801021 DUP . . . PASS SVTYPE DUP SVLEN 13226 READS 15 GT 0/1 chr21 32842805 DUP . . . PASS SVTYPE DUP SVLEN 4282 READS 20 GT 0/1 chr21 33250495 DUP . . . PASS SVTYPE DUP SVLEN 3418 READS 32 GT 0/1 chr21 33387854 DUP . . . PASS SVTYPE DUP SVLEN 82775 READS 53 GT 0/1 chr21 33800493 DUP . . . PASS SVTYPE DUP SVLEN 12579 READS 228 GT 0/1 chr21 33817955 DUP . . . PASS SVTYPE DUP SVLEN 8926 READS 475 GT 1/1 chr21 33859819 DUP . . . PASS SVTYPE DUP SVLEN 47103 READS 22 GT 0/1 chr21 33867161 DUP . . . PASS SVTYPE DUP SVLEN 55054 READS 19 GT 0/1 chr21 33985037 DUP . . . PASS SVTYPE DUP SVLEN 11215 READS 223 GT 0/1 chr21 34047662 DUP . . . PASS SVTYPE DUP SVLEN 75859 READS 26 GT 0/1 chr21 34180847 DUP . . . PASS SVTYPE DUP SVLEN 2299 READS 33 GT 0/1 chr21 34204194 DUP . . . PASS SVTYPE DUP SVLEN 61640 READS 23 GT 0/1 chr21 34293160 DUP . . . PASS SVTYPE DUP SVLEN 22285 READS 13 GT 0/1 chr21 34360645 DUP . . . PASS SVTYPE DUP SVLEN 2302 READS 21 GT 0/1 chr21 34404309 DUP . . . PASS SVTYPE DUP SVLEN 9820 READS 30 GT 0/1 chr21 34421898 DUP . . . PASS SVTYPE DUP SVLEN 6969 READS 17 GT 0/1 chr21 34477204 DUP . . . PASS SVTYPE DUP SVLEN 3769 READS 567 GT 0/1 chr21 34517184 DUP . . . PASS SVTYPE DUP SVLEN 1899 READS 42 GT 0/1 chr21 34555855 DUP . . . PASS SVTYPE DUP SVLEN 6001 READS 47 GT 0/1 chr21 34644082 DUP . . . PASS SVTYPE DUP SVLEN 35650 READS 19 GT 0/1 chr21 34660001 DUP . . . PASS SVTYPE DUP SVLEN 5654 READS 21 GT 0/1 chr21 34694161 DUP . . . PASS SVTYPE DUP SVLEN 2345 READS 70 GT 0/1 chr21 34694267 DUP . . . PASS SVTYPE DUP SVLEN 4118 READS 18 GT 0/1 chr21 34737057 DUP . . . PASS SVTYPE DUP SVLEN 7501 READS 35 GT 0/1 chr21 34768787 DUP . . . PASS SVTYPE DUP SVLEN 13110 READS 20 GT 0/1 chr21 34783173 DUP . . . PASS SVTYPE DUP SVLEN 2322 READS 246 GT 0/1 chr21 34847200 DUP . . . PASS SVTYPE DUP SVLEN 12701 READS 24 GT 0/1 chr21 34921299 DUP . . . PASS SVTYPE DUP SVLEN 8401 READS 21 GT 0/1 chr21 35383200 DUP . . . PASS SVTYPE DUP SVLEN 5001 READS 43 GT 0/1 chr21 35383916 DUP . . . PASS SVTYPE DUP SVLEN 3326 READS 29 GT 0/1 chr21 35416864 DUP . . . PASS SVTYPE DUP SVLEN 15753 READS 19 GT 0/1 chr21 35512661 DUP . . . PASS SVTYPE DUP SVLEN 10648 READS 28 GT 0/1 chr21 35528078 DUP . . . PASS SVTYPE DUP SVLEN 18200 READS 43 GT 0/1 chr21 35634585 DUP . . . PASS SVTYPE DUP SVLEN 82882 READS 32 GT 0/1 chr21 35939413 DUP . . . PASS SVTYPE DUP SVLEN 2146 READS 17 GT 0/1 chr21 36031699 DUP . . . PASS SVTYPE DUP SVLEN 4302 READS 15 GT 0/1 chr21 36041690 DUP . . . PASS SVTYPE DUP SVLEN 5001 READS 22 GT 0/1 chr21 36051246 DUP . . . PASS SVTYPE DUP SVLEN 30216 READS 48 GT 0/1 chr21 36092362 DUP . . . PASS SVTYPE DUP SVLEN 28101 READS 40 GT 0/1 chr21 36258024 DUP . . . PASS SVTYPE DUP SVLEN 4427 READS 15 GT 0/1 chr21 36277300 DUP . . . PASS SVTYPE DUP SVLEN 31100 READS 23 GT 0/1 chr21 36297663 DUP . . . PASS SVTYPE DUP SVLEN 3205 READS 63 GT 0/1 chr21 36380025 DUP . . . PASS SVTYPE DUP SVLEN 77474 READS 26 GT 0/1 chr21 36458337 DUP . . . PASS SVTYPE DUP SVLEN 1402 READS 49 GT 0/1 chr21 36485090 DUP . . . PASS SVTYPE DUP SVLEN 3589 READS 21 GT 0/1 chr21 36973801 DUP . . . PASS SVTYPE DUP SVLEN 14823 READS 46 GT 0/1 chr21 36995160 DUP . . . PASS SVTYPE DUP SVLEN 64399 READS 18 GT 0/1 chr21 37002142 DUP . . . PASS SVTYPE DUP SVLEN 17700 READS 25 GT 0/1 chr21 37033229 DUP . . . PASS SVTYPE DUP SVLEN 67108 READS 23 GT 0/1 chr21 37174801 DUP . . . PASS SVTYPE DUP SVLEN 3600 READS 30 GT 0/1 chr21 37185130 DUP . . . PASS SVTYPE DUP SVLEN 14243 READS 33 GT 0/1 chr21 37244129 DUP . . . PASS SVTYPE DUP SVLEN 77238 READS 53 GT 0/1 chr21 37387525 DUP . . . PASS SVTYPE DUP SVLEN 2068 READS 192 GT 0/1 chr21 37404267 DUP . . . PASS SVTYPE DUP SVLEN 1242 READS 31 GT 0/1 chr21 37782214 DUP . . . PASS SVTYPE DUP SVLEN 37607 READS 23 GT 0/1 chr21 37812710 DUP . . . PASS SVTYPE DUP SVLEN 3357 READS 17 GT 0/1 chr21 37839589 DUP . . . PASS SVTYPE DUP SVLEN 17496 READS 23 GT 0/1 chr21 37857575 DUP . . . PASS SVTYPE DUP SVLEN 5361 READS 382 GT 0/1 chr21 37857576 DUP . . . PASS SVTYPE DUP SVLEN 5156 READS 0 GT 0/1 chr21 37857726 DUP . . . PASS SVTYPE DUP SVLEN 5207 READS 0 GT 0/0 chr21 37879843 DUP . . . PASS SVTYPE DUP SVLEN 4900 READS 15 GT 0/1 chr21 37911382 DUP . . . PASS SVTYPE DUP SVLEN 1399 READS 33 GT 0/1 chr21 37922877 DUP . . . PASS SVTYPE DUP SVLEN 15870 READS 15 GT 0/1 chr21 37928999 DUP . . . PASS SVTYPE DUP SVLEN 3635 READS 211 GT 0/1 chr21 37963484 DUP . . . PASS SVTYPE DUP SVLEN 3260 READS 147 GT 0/1 chr21 38160029 DUP . . . PASS SVTYPE DUP SVLEN 17826 READS 21 GT 0/1 chr21 38195786 DUP . . . PASS SVTYPE DUP SVLEN 1199 READS 218 GT 0/1 chr21 38296903 DUP . . . PASS SVTYPE DUP SVLEN 8923 READS 20 GT 0/1 chr21 38313402 DUP . . . PASS SVTYPE DUP SVLEN 3920 READS 17 GT 0/1 chr21 38342066 DUP . . . PASS SVTYPE DUP SVLEN 41374 READS 32 GT 0/1 chr21 38345143 DUP . . . PASS SVTYPE DUP SVLEN 1989 READS 22 GT 0/1 chr21 38394965 DUP . . . PASS SVTYPE DUP SVLEN 91380 READS 43 GT 0/1 chr21 38486556 DUP . . . PASS SVTYPE DUP SVLEN 2247 READS 18 GT 0/1 chr21 38739899 DUP . . . PASS SVTYPE DUP SVLEN 80300 READS 54 GT 0/1 chr21 38831529 DUP . . . PASS SVTYPE DUP SVLEN 5127 READS 25 GT 0/1 chr21 39084801 DUP . . . PASS SVTYPE DUP SVLEN 46573 READS 22 GT 0/1 chr21 39335434 DUP . . . PASS SVTYPE DUP SVLEN 28891 READS 23 GT 0/1 chr21 39483260 DUP . . . PASS SVTYPE DUP SVLEN 93915 READS 20 GT 0/1 chr21 39846571 DUP . . . PASS SVTYPE DUP SVLEN 29006 READS 17 GT 0/1 chr21 39907024 DUP . . . PASS SVTYPE DUP SVLEN 10706 READS 46 GT 0/1 chr21 39923186 DUP . . . PASS SVTYPE DUP SVLEN 92603 READS 107 GT 0/1 chr21 40053564 DUP . . . PASS SVTYPE DUP SVLEN 41508 READS 15 GT 0/1 chr21 40103879 DUP . . . PASS SVTYPE DUP SVLEN 43483 READS 72 GT 0/1 chr21 40345403 DUP . . . PASS SVTYPE DUP SVLEN 21495 READS 45 GT 0/1 chr21 40456135 DUP . . . PASS SVTYPE DUP SVLEN 22493 READS 45 GT 0/1 chr21 40555800 DUP . . . PASS SVTYPE DUP SVLEN 28200 READS 38 GT 0/1 chr21 40668786 DUP . . . PASS SVTYPE DUP SVLEN 1625 READS 220 GT 0/1 chr21 40675942 DUP . . . PASS SVTYPE DUP SVLEN 17372 READS 28 GT 0/1 chr21 40714340 DUP . . . PASS SVTYPE DUP SVLEN 2296 READS 213 GT 0/1 chr21 40733023 DUP . . . PASS SVTYPE DUP SVLEN 10631 READS 447 GT 0/1 chr21 40833992 DUP . . . PASS SVTYPE DUP SVLEN 89809 READS 22 GT 0/1 chr21 40940200 DUP . . . PASS SVTYPE DUP SVLEN 33001 READS 21 GT 0/1 chr21 40981640 DUP . . . PASS SVTYPE DUP SVLEN 5844 READS 22 GT 0/1 chr21 41275632 DUP . . . PASS SVTYPE DUP SVLEN 2189 READS 29 GT 0/1 chr21 41289891 DUP . . . PASS SVTYPE DUP SVLEN 90255 READS 23 GT 0/1 chr21 41529720 DUP . . . PASS SVTYPE DUP SVLEN 87105 READS 23 GT 0/1 chr21 41853205 DUP . . . PASS SVTYPE DUP SVLEN 8311 READS 20 GT 0/1 chr21 41867196 DUP . . . PASS SVTYPE DUP SVLEN 42066 READS 45 GT 0/1 chr21 42274251 DUP . . . PASS SVTYPE DUP SVLEN 1397 READS 53 GT 0/1 chr21 42364482 DUP . . . PASS SVTYPE DUP SVLEN 1899 READS 68 GT 0/1 chr21 42384182 DUP . . . PASS SVTYPE DUP SVLEN 1699 READS 19 GT 0/1 chr21 42446438 DUP . . . PASS SVTYPE DUP SVLEN 2757 READS 16 GT 0/1 chr21 42726273 DUP . . . PASS SVTYPE DUP SVLEN 36815 READS 25 GT 0/1 chr21 42729837 DUP . . . PASS SVTYPE DUP SVLEN 22502 READS 25 GT 0/1 chr21 42782629 DUP . . . PASS SVTYPE DUP SVLEN 43921 READS 49 GT 0/1 chr21 42827368 DUP . . . PASS SVTYPE DUP SVLEN 71962 READS 23 GT 0/1 chr21 43010102 DUP . . . PASS SVTYPE DUP SVLEN 17166 READS 48 GT 0/1 chr21 43067929 DUP . . . PASS SVTYPE DUP SVLEN 8193 READS 23 GT 0/1 chr21 43134930 DUP . . . PASS SVTYPE DUP SVLEN 4622 READS 38 GT 0/1 chr21 43177640 DUP . . . PASS SVTYPE DUP SVLEN 29246 READS 25 GT 0/1 chr21 43276783 DUP . . . PASS SVTYPE DUP SVLEN 5654 READS 24 GT 0/1 chr21 43374483 DUP . . . PASS SVTYPE DUP SVLEN 1199 READS 35 GT 0/1 chr21 43426376 DUP . . . PASS SVTYPE DUP SVLEN 8087 READS 20 GT 0/1 chr21 43477265 DUP . . . PASS SVTYPE DUP SVLEN 8467 READS 27 GT 0/1 chr21 43603183 DUP . . . PASS SVTYPE DUP SVLEN 1499 READS 47 GT 0/1 chr21 43677830 DUP . . . PASS SVTYPE DUP SVLEN 46523 READS 24 GT 0/1 chr21 43712483 DUP . . . PASS SVTYPE DUP SVLEN 2099 READS 63 GT 0/1 chr21 43759078 DUP . . . PASS SVTYPE DUP SVLEN 33711 READS 24 GT 0/1 chr21 43790550 DUP . . . PASS SVTYPE DUP SVLEN 11651 READS 14 GT 0/1 chr21 43830583 DUP . . . PASS SVTYPE DUP SVLEN 1399 READS 132 GT 0/1 chr21 43834199 DUP . . . PASS SVTYPE DUP SVLEN 59001 READS 27 GT 0/1 chr21 44054900 DUP . . . PASS SVTYPE DUP SVLEN 1301 READS 18 GT 0/1 chr21 44061668 DUP . . . PASS SVTYPE DUP SVLEN 43457 READS 18 GT 0/1 chr21 44109942 DUP . . . PASS SVTYPE DUP SVLEN 7968 READS 27 GT 0/1 chr21 44140693 DUP . . . PASS SVTYPE DUP SVLEN 11944 READS 20 GT 0/1 chr21 44247272 DUP . . . PASS SVTYPE DUP SVLEN 25598 READS 22 GT 0/1 chr21 44258769 DUP . . . PASS SVTYPE DUP SVLEN 64151 READS 12 GT 0/1 chr21 44355257 DUP . . . PASS SVTYPE DUP SVLEN 10618 READS 42 GT 0/1 chr21 44963686 DUP . . . PASS SVTYPE DUP SVLEN 11444 READS 53 GT 0/1 chr21 44983478 DUP . . . PASS SVTYPE DUP SVLEN 3664 READS 217 GT 0/1 chr21 45019899 DUP . . . PASS SVTYPE DUP SVLEN 5702 READS 26 GT 0/1 chr21 45023823 DUP . . . PASS SVTYPE DUP SVLEN 2099 READS 31 GT 0/1 chr21 45027526 DUP . . . PASS SVTYPE DUP SVLEN 11789 READS 26 GT 0/1 chr21 45031626 DUP . . . PASS SVTYPE DUP SVLEN 12915 READS 24 GT 0/1 chr21 45039444 DUP . . . PASS SVTYPE DUP SVLEN 45118 READS 19 GT 0/1 chr21 45100456 DUP . . . PASS SVTYPE DUP SVLEN 81975 READS 21 GT 0/1 chr21 45155220 DUP . . . PASS SVTYPE DUP SVLEN 12034 READS 968 GT 1/1 chr21 45205938 DUP . . . PASS SVTYPE DUP SVLEN 53565 READS 24 GT 0/1 chr21 45235399 DUP . . . PASS SVTYPE DUP SVLEN 3401 READS 15 GT 0/1 chr21 45260244 DUP . . . PASS SVTYPE DUP SVLEN 88470 READS 26 GT 0/1 chr21 45322431 DUP . . . PASS SVTYPE DUP SVLEN 30626 READS 32 GT 0/1 chr21 46080921 DUP . . . PASS SVTYPE DUP SVLEN 13265 READS 24 GT 0/1 chr21 46085481 DUP . . . PASS SVTYPE DUP S

bioinfo89 commented 3 years ago

How can I extract the True & False negative values?

Best, Khyati Chandratre

On 11 Sep 2020, at 10:02 PM, stat-lab notifications@github.com wrote:

In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs?

Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691391935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPF2XJGSGXBLR7R6DF53SFLQGBANCNFSM4RF5G6QA.

stat-lab commented 3 years ago

I extracted DUP lines from Simchr21.truth.vcf to generate Simchr21.truth.DUP.vcf and converted Delly_DUP_M.txt to a vcf file (Delly_DUP_M.vcf). I run these files with evaluate_SV_callers.pl (i.e., evaluate_SV_callers.pl -r2 Simchr21.truth.DUP.vcf Delly_DUP_M.vcf). The resulting evaluated file is as follows:

Ref-DEL: 0 tinny (<= 100 bp): 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-INS: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-DUP: 674 short (<=1.0 kp): 170 middle (<= 100 kb): 416 large (> 100 kb): 88 Ref-INV: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0

<< Simchr21 >>

DUP

        <Number of supporting reads>
        2   3   4   5   6   7   8   9   10  12

Call (A) 397 396 396 396 395 394 392 392 390 388 Recall (A) 58.9 58.7 58.7 58.7 58.6 58.4 58.1 58.1 57.8 57.5
Precis (A) 100 100 100 100 100 100 100 100 100 100 Call (S) 0 0 0 0 0 0 0 0 0 0
Recall (S) 0 0 0 0 0 0 0 0 0 0
Precis (S) 0 0 0 0 0 0 0 0 0 0
Call (M) 397 396 396 396 395 394 392 392 390 388 Recall (M) 95.1 94.9 94.9 94.9 94.7 94.4 93.9 93.9 93.5 93
Precis (M) 100 100 100 100 100 100 100 100 100 100 Call (L) 0 0 0 0 0 0 0 0 0 0
Recall (L) 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 Precis (L) 0 0 0 0 0 0 0 0 0 0

The number of DUP calls was 397, which was smaller than the original number 417 in the Delly_DUP_M.vcf because highly overlapped DUP calls are contained in the Delly_DUP_M.vcf. Our evaluation removes SV calls with reciprocal > 80% overlap. Otherwise, one of the two overlapping calls would be regarded as false positive even if both the calls match a reference SV. The precision did not exceed 100. Some overlapped DUPs in the other size range might disturb the evaluation. If you want to obtain precise results for evaluation, your input SV calls should be prepared reducing overlaps.

2020/09/12 13:55、bioinfo89 notifications@github.comのメール:

How can I extract the True & False negative values?

Best, Khyati Chandratre

On 11 Sep 2020, at 10:02 PM, stat-lab notifications@github.com wrote:

In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs?

Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls).

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691391935, or unsubscribe https://github.com/notifications/unsubscribe-auth/AIAOPF2XJGSGXBLR7R6DF53SFLQGBANCNFSM4RF5G6QA.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/9#issuecomment-691409816, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIBV3BFCYLD6I5ZDAY3P73SFL5MHANCNFSM4RF5G6QA.

bioinfo89 commented 3 years ago

Yeah, that sounds like a good explanation as to why I am getting the output. SV calling tools do not have any parameter which calls with an overlap cut-off. The overlap cut-off is usually offered by tools which can compare VCFs like your script, so I am not sure how I can reduce the overlap calls this way. Plus the Delly VCF test file is also obtained using simulated data with known variants imputed.

So, in such case where it shows >100% of precision, should I simply consider it as 100%?

Best, Khyati Chandratre

On 12 Sep 2020, at 12:59 AM, stat-lab notifications@github.com wrote:

I extracted DUP lines from Simchr21.truth.vcf to generate Simchr21.truth.DUP.vcf and converted Delly_DUP_M.txt to a vcf file (Delly_DUP_M.vcf). I run these files with evaluate_SV_callers.pl (i.e., evaluate_SV_callers.pl -r2 Simchr21.truth.DUP.vcf Delly_DUP_M.vcf). The resulting evaluated file is as follows:

Ref-DEL: 0 tinny (<= 100 bp): 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-INS: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-DUP: 674 short (<=1.0 kp): 170 middle (<= 100 kb): 416 large (> 100 kb): 88 Ref-INV: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0

<< Simchr21 >>

DUP

2 3 4 5 6 7 8 9 10 12 Call (A) 397 396 396 396 395 394 392 392 390 388 Recall (A) 58.9 58.7 58.7 58.7 58.6 58.4 58.1 58.1 57.8 57.5 Precis (A) 100 100 100 100 100 100 100 100 100 100 Call (S) 0 0 0 0 0 0 0 0 0 0 Recall (S) 0 0 0 0 0 0 0 0 0 0 Precis (S) 0 0 0 0 0 0 0 0 0 0 Call (M) 397 396 396 396 395 394 392 392 390 388 Recall (M) 95.1 94.9 94.9 94.9 94.7 94.4 93.9 93.9 93.5 93 Precis (M) 100 100 100 100 100 100 100 100 100 100 Call (L) 0 0 0 0 0 0 0 0 0 0 Recall (L) 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 Precis (L) 0 0 0 0 0 0 0 0 0 0 The number of DUP calls was 397, which was smaller than the original number 417 in the Delly_DUP_M.vcf because highly overlapped DUP calls are contained in the Delly_DUP_M.vcf. Our evaluation removes SV calls with reciprocal > 80% overlap. Otherwise, one of the two overlapping calls would be regarded as false positive even if both the calls match a reference SV. The precision did not exceed 100. Some overlapped DUPs in the other size range might disturb the evaluation. If you want to obtain precise results for evaluation, your input SV calls should be prepared reducing overlaps. > 2020/09/12 13:55、bioinfo89 のメール: > > > How can I extract the True & False negative values? > > Best, > Khyati Chandratre > > > > > > On 11 Sep 2020, at 10:02 PM, stat-lab wrote: > > > > > > In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs? > > > > Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls). > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub , or unsubscribe . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or unsubscribe .
stat-lab commented 3 years ago

Yes, you should do so.

2020/09/13 2:49、bioinfo89 notifications@github.comのメール:

Yeah, that sounds like a good explanation as to why I am getting the output. SV calling tools do not have any parameter which calls with an overlap cut-off. The overlap cut-off is usually offered by tools which can compare VCFs like your script, so I am not sure how I can reduce the overlap calls this way. Plus the Delly VCF test file is also obtained using simulated data with known variants imputed.

So, in such case where it shows >100% of precision, should I simply consider it as 100%?

Best, Khyati Chandratre

On 12 Sep 2020, at 12:59 AM, stat-lab notifications@github.com wrote:

I extracted DUP lines from Simchr21.truth.vcf to generate Simchr21.truth.DUP.vcf and converted Delly_DUP_M.txt to a vcf file (Delly_DUP_M.vcf). I run these files with evaluate_SV_callers.pl (i.e., evaluate_SV_callers.pl -r2 Simchr21.truth.DUP.vcf Delly_DUP_M.vcf). The resulting evaluated file is as follows:

Ref-DEL: 0 tinny (<= 100 bp): 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-INS: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-DUP: 674 short (<=1.0 kp): 170 middle (<= 100 kb): 416 large (> 100 kb): 88 Ref-INV: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0

<< Simchr21 >>

DUP

2 3 4 5 6 7 8 9 10 12 Call (A) 397 396 396 396 395 394 392 392 390 388 Recall (A) 58.9 58.7 58.7 58.7 58.6 58.4 58.1 58.1 57.8 57.5 Precis (A) 100 100 100 100 100 100 100 100 100 100 Call (S) 0 0 0 0 0 0 0 0 0 0 Recall (S) 0 0 0 0 0 0 0 0 0 0 Precis (S) 0 0 0 0 0 0 0 0 0 0 Call (M) 397 396 396 396 395 394 392 392 390 388 Recall (M) 95.1 94.9 94.9 94.9 94.7 94.4 93.9 93.9 93.5 93 Precis (M) 100 100 100 100 100 100 100 100 100 100 Call (L) 0 0 0 0 0 0 0 0 0 0 Recall (L) 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 Precis (L) 0 0 0 0 0 0 0 0 0 0 The number of DUP calls was 397, which was smaller than the original number 417 in the Delly_DUP_M.vcf because highly overlapped DUP calls are contained in the Delly_DUP_M.vcf. Our evaluation removes SV calls with reciprocal > 80% overlap. Otherwise, one of the two overlapping calls would be regarded as false positive even if both the calls match a reference SV. The precision did not exceed 100. Some overlapped DUPs in the other size range might disturb the evaluation. If you want to obtain precise results for evaluation, your input SV calls should be prepared reducing overlaps. > 2020/09/12 13:55、bioinfo89 のメール: > > > How can I extract the True & False negative values? > > Best, > Khyati Chandratre > > > > > > On 11 Sep 2020, at 10:02 PM, stat-lab wrote: > > > > > > In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs? > > > > Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls). > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub , or unsubscribe . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or unsubscribe .

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bioinfo89 commented 3 years ago

Thanks !How do I extract the true negative and false negative values from your script?

Best,

Khyati Chandratre

On Sat, Sep 12, 2020 at 9:08 PM, stat-labnotifications@github.com wrote:

Yes, you should do so.

2020/09/13 2:49、bioinfo89 notifications@github.comのメール:

Yeah, that sounds like a good explanation as to why I am getting the output. SV calling tools do not have any parameter which calls with an overlap cut-off. The overlap cut-off is usually offered by tools which can compare VCFs like your script, so I am not sure how I can reduce the overlap calls this way. Plus the Delly VCF test file is also obtained using simulated data with known variants imputed.

So, in such case where it shows >100% of precision, should I simply consider it as 100%?

Best, Khyati Chandratre

On 12 Sep 2020, at 12:59 AM, stat-lab notifications@github.com wrote:

I extracted DUP lines from Simchr21.truth.vcf to generate Simchr21.truth.DUP.vcf and converted Delly_DUP_M.txt to a vcf file (Delly_DUP_M.vcf). I run these files with evaluate_SV_callers.pl (i.e., evaluate_SV_callers.pl -r2 Simchr21.truth.DUP.vcf Delly_DUP_M.vcf). The resulting evaluated file is as follows:

Ref-DEL: 0 tinny (<= 100 bp): 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-INS: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-DUP: 674 short (<=1.0 kp): 170 middle (<= 100 kb): 416 large (> 100 kb): 88 Ref-INV: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0

<< Simchr21 >>

DUP

2 3 4 5 6 7 8 9 10 12 Call (A) 397 396 396 396 395 394 392 392 390 388 Recall (A) 58.9 58.7 58.7 58.7 58.6 58.4 58.1 58.1 57.8 57.5 Precis (A) 100 100 100 100 100 100 100 100 100 100 Call (S) 0 0 0 0 0 0 0 0 0 0 Recall (S) 0 0 0 0 0 0 0 0 0 0 Precis (S) 0 0 0 0 0 0 0 0 0 0 Call (M) 397 396 396 396 395 394 392 392 390 388 Recall (M) 95.1 94.9 94.9 94.9 94.7 94.4 93.9 93.9 93.5 93 Precis (M) 100 100 100 100 100 100 100 100 100 100 Call (L) 0 0 0 0 0 0 0 0 0 0 Recall (L) 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 Precis (L) 0 0 0 0 0 0 0 0 0 0 The number of DUP calls was 397, which was smaller than the original number 417 in the Delly_DUP_M.vcf because highly overlapped DUP calls are contained in the Delly_DUP_M.vcf. Our evaluation removes SV calls with reciprocal > 80% overlap. Otherwise, one of the two overlapping calls would be regarded as false positive even if both the calls match a reference SV. The precision did not exceed 100. Some overlapped DUPs in the other size range might disturb the evaluation. If you want to obtain precise results for evaluation, your input SV calls should be prepared reducing overlaps. > 2020/09/12 13:55、bioinfo89 のメール: > > > How can I extract the True & False negative values? > > Best, > Khyati Chandratre > > > > > > On 11 Sep 2020, at 10:02 PM, stat-lab wrote: > > > > > > In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs? > > > > Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls). > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub , or unsubscribe . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or unsubscribe .

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stat-lab commented 3 years ago

I will update the script that can output true positive and/or false positive calls with specified options in the near future.

2020/09/13 14:01、bioinfo89 notifications@github.comのメール:

Thanks !How do I extract the true negative and false negative values from your script?

Best,

Khyati Chandratre

On Sat, Sep 12, 2020 at 9:08 PM, stat-labnotifications@github.com wrote:

Yes, you should do so.

2020/09/13 2:49、bioinfo89 notifications@github.comのメール:

Yeah, that sounds like a good explanation as to why I am getting the output. SV calling tools do not have any parameter which calls with an overlap cut-off. The overlap cut-off is usually offered by tools which can compare VCFs like your script, so I am not sure how I can reduce the overlap calls this way. Plus the Delly VCF test file is also obtained using simulated data with known variants imputed.

So, in such case where it shows >100% of precision, should I simply consider it as 100%?

Best, Khyati Chandratre

On 12 Sep 2020, at 12:59 AM, stat-lab notifications@github.com wrote:

I extracted DUP lines from Simchr21.truth.vcf to generate Simchr21.truth.DUP.vcf and converted Delly_DUP_M.txt to a vcf file (Delly_DUP_M.vcf). I run these files with evaluate_SV_callers.pl (i.e., evaluate_SV_callers.pl -r2 Simchr21.truth.DUP.vcf Delly_DUP_M.vcf). The resulting evaluated file is as follows:

Ref-DEL: 0 tinny (<= 100 bp): 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-INS: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-DUP: 674 short (<=1.0 kp): 170 middle (<= 100 kb): 416 large (> 100 kb): 88 Ref-INV: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0

<< Simchr21 >>

DUP

2 3 4 5 6 7 8 9 10 12 Call (A) 397 396 396 396 395 394 392 392 390 388 Recall (A) 58.9 58.7 58.7 58.7 58.6 58.4 58.1 58.1 57.8 57.5 Precis (A) 100 100 100 100 100 100 100 100 100 100 Call (S) 0 0 0 0 0 0 0 0 0 0 Recall (S) 0 0 0 0 0 0 0 0 0 0 Precis (S) 0 0 0 0 0 0 0 0 0 0 Call (M) 397 396 396 396 395 394 392 392 390 388 Recall (M) 95.1 94.9 94.9 94.9 94.7 94.4 93.9 93.9 93.5 93 Precis (M) 100 100 100 100 100 100 100 100 100 100 Call (L) 0 0 0 0 0 0 0 0 0 0 Recall (L) 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 Precis (L) 0 0 0 0 0 0 0 0 0 0 The number of DUP calls was 397, which was smaller than the original number 417 in the Delly_DUP_M.vcf because highly overlapped DUP calls are contained in the Delly_DUP_M.vcf. Our evaluation removes SV calls with reciprocal > 80% overlap. Otherwise, one of the two overlapping calls would be regarded as false positive even if both the calls match a reference SV. The precision did not exceed 100. Some overlapped DUPs in the other size range might disturb the evaluation. If you want to obtain precise results for evaluation, your input SV calls should be prepared reducing overlaps. > 2020/09/12 13:55、bioinfo89 のメール: > > > How can I extract the True & False negative values? > > Best, > Khyati Chandratre > > > > > > On 11 Sep 2020, at 10:02 PM, stat-lab wrote: > > > > > > In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs? > > > > Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls). > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub , or unsubscribe . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or unsubscribe .

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bioinfo89 commented 3 years ago

Yes, that would be great. Thanks! I would suggest to add true positive rates and False positive rates so that it can be useful in creating useful graphs like ROC form the output directly.

Best, Khyati Chandratre

On 13 Sep 2020, at 12:38 AM, stat-lab notifications@github.com wrote:

I will update the script that can output true positive and/or false positive calls with specified options in the near future.

2020/09/13 14:01、bioinfo89 notifications@github.comのメール:

Thanks !How do I extract the true negative and false negative values from your script?

Best,

Khyati Chandratre

On Sat, Sep 12, 2020 at 9:08 PM, stat-labnotifications@github.com wrote:

Yes, you should do so.

2020/09/13 2:49、bioinfo89 notifications@github.comのメール:

Yeah, that sounds like a good explanation as to why I am getting the output. SV calling tools do not have any parameter which calls with an overlap cut-off. The overlap cut-off is usually offered by tools which can compare VCFs like your script, so I am not sure how I can reduce the overlap calls this way. Plus the Delly VCF test file is also obtained using simulated data with known variants imputed.

So, in such case where it shows >100% of precision, should I simply consider it as 100%?

Best, Khyati Chandratre

On 12 Sep 2020, at 12:59 AM, stat-lab notifications@github.com wrote:

I extracted DUP lines from Simchr21.truth.vcf to generate Simchr21.truth.DUP.vcf and converted Delly_DUP_M.txt to a vcf file (Delly_DUP_M.vcf). I run these files with evaluate_SV_callers.pl (i.e., evaluate_SV_callers.pl -r2 Simchr21.truth.DUP.vcf Delly_DUP_M.vcf). The resulting evaluated file is as follows:

Ref-DEL: 0 tinny (<= 100 bp): 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-INS: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0 Ref-DUP: 674 short (<=1.0 kp): 170 middle (<= 100 kb): 416 large (> 100 kb): 88 Ref-INV: 0 short (<=1.0 kp): 0 middle (<= 100 kb): 0 large (> 100 kb): 0

<< Simchr21 >>

DUP

2 3 4 5 6 7 8 9 10 12 Call (A) 397 396 396 396 395 394 392 392 390 388 Recall (A) 58.9 58.7 58.7 58.7 58.6 58.4 58.1 58.1 57.8 57.5 Precis (A) 100 100 100 100 100 100 100 100 100 100 Call (S) 0 0 0 0 0 0 0 0 0 0 Recall (S) 0 0 0 0 0 0 0 0 0 0 Precis (S) 0 0 0 0 0 0 0 0 0 0 Call (M) 397 396 396 396 395 394 392 392 390 388 Recall (M) 95.1 94.9 94.9 94.9 94.7 94.4 93.9 93.9 93.5 93 Precis (M) 100 100 100 100 100 100 100 100 100 100 Call (L) 0 0 0 0 0 0 0 0 0 0 Recall (L) 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.1 Precis (L) 0 0 0 0 0 0 0 0 0 0 The number of DUP calls was 397, which was smaller than the original number 417 in the Delly_DUP_M.vcf because highly overlapped DUP calls are contained in the Delly_DUP_M.vcf. Our evaluation removes SV calls with reciprocal > 80% overlap. Otherwise, one of the two overlapping calls would be regarded as false positive even if both the calls match a reference SV. The precision did not exceed 100. Some overlapped DUPs in the other size range might disturb the evaluation. If you want to obtain precise results for evaluation, your input SV calls should be prepared reducing overlaps. > 2020/09/12 13:55、bioinfo89 のメール: > > > How can I extract the True & False negative values? > > Best, > Khyati Chandratre > > > > > > On 11 Sep 2020, at 10:02 PM, stat-lab wrote: > > > > > > In your vcf file, for example, the line at position chr21:16106490 has no SVTYPE tag. Although the lines at the position chr21:15830838 and chr21:15852911 have SVTYPE=DEL, these DELs are short 1-bp dels, which are not considered as the reference SVs. Does the vcf file contain >= 30 bp DELs? > > > > Regarding true positive calls, you can calculate these simply by multiplying the number of calls with the precision * 0.01. The false positive calls are (the number of calls) - (true positive calls). > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub , or unsubscribe . > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub , or unsubscribe . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or unsubscribe .

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stat-lab commented 3 years ago

I updated the script evaluate_SV_callers.pl, which can output TP, FP, or TP/FP calls with a newly added option -of (0: no output, 1: TP calls, 2: FP calls, 3: both with TP or FP label at the line heads. Please try it.

bioinfo89 commented 3 years ago

OK great! I will try it. Thanks Best, Khyati Chandratre

On 23 Sep 2020, at 4:20 AM, stat-lab notifications@github.com wrote:

I updated the script evaluate_SV_callers.pl, which can output TP, FP, or TP/FP calls with a newly added option -of (0: no output, 1: TP calls, 2: FP calls, 3: both with TP or FP label at the line heads. Please try it.

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