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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Difference in number of integrations in virus summary vs. VCF #658

Closed AqsaAlam closed 5 months ago

AqsaAlam commented 6 months ago

Hi!

I am analyzing results from virusbreakend and noticed that the number of integrations in the summary output is different than that in the VCF. For example, the summary reported 57 integrations for my sample, but the VCF is showing 92 (only looking at human chromosomes). Why is that?

d-cameron commented 6 months ago

How are you counting the 57 vs 92? A single integration site can have 2 breakpoints (left and right size of the insertion in human coordinate space) which is 4 VCF BND records.

AqsaAlam commented 6 months ago

Hi!

Thanks for your quick response!

The vcf summary output says "integrations = 57" (I've attached the file). The vcf file has 184 entries, 92 of which are human chromosome breakpoints. (I've also attached the file).

I've confirmed they are the same sample.

Cheers,

Aqsa Alam

From: Daniel Cameron @.> Sent: Wednesday, April 17, 2024 11:02 PM To: PapenfussLab/gridss @.> Cc: Aqsa Alam @.>; Author @.> Subject: Re: [PapenfussLab/gridss] Difference in number of integrations in virus summary vs. VCF (Issue #658)

How are you counting the 57 vs 92? A single integration site can have 2 breakpoints (left and right size of the insertion in human coordinate space) which is 4 VCF BND records.

- Reply to this email directly, view it on GitHubhttps://github.com/PapenfussLab/gridss/issues/658#issuecomment-2062906469, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AXFDL4PMRAIU2OTCXLSMGODY54ZSRAVCNFSM6AAAAABGMB2GXSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRSHEYDMNBWHE. You are receiving this because you authored the thread.Message ID: @.**@.>>

fileformat=VCFv4.2

"##FILTER=<ID=ASSEMBLY_BIAS,Description=""Mismatch between number of directly supporting reads and reads supporting via assembly."">"
"##FILTER=<ID=ASSEMBLY_ONLY,Description=""Variant is supported only by assembly evidence."">"
"##FILTER=<ID=ASSEMBLY_TOO_FEW_READ,Description=""Not enough reads contribute to this assembly as specified by 'assembly.minReads'"">"
"##FILTER=<ID=ASSEMBLY_TOO_SHORT,Description=""This assembly is shorter than a read length"">"
"##FILTER=<ID=INSUFFICIENT_SUPPORT,Description=""Does not reach the required threshold quality for calling as specified by 'variantcalling.minScore'"">"
"##FILTER=<ID=LOW_MAPQ,Description=""Mapping location may be ambiguous."">"
"##FILTER=<ID=LOW_QUAL,Description=""Low quality call as specified by 'variantcalling.lowQuality'"">"
"##FILTER=<ID=NO_ASSEMBLY,Description=""No assembly supporting this variant could be found."">"
"##FILTER=<ID=NO_RP,Description=""Variant does not have any direct read pair support."">"
"##FILTER=<ID=NO_SR,Description=""Variant does not have any direct split read support."">"
"##FILTER=<ID=REF,Description=""Breakpoint corresponds to reference allele"">"
"##FILTER=<ID=SINGLE_ASSEMBLY,Description=""Only one side of the breakpoint could be assembled."">"
"##FILTER=<ID=SINGLE_SUPPORT,Description=""Supported by fewer than 'variantcalling.minReads' fragments"">"
"##FILTER=<ID=SMALL_EVENT,Description=""Event size is smaller than the minimum reportable size specified by 'variantcalling.minSize'"">"
"##FORMAT=<ID=AF,Number=A,Type=Float,Description=""Allele fraction"">"
"##FORMAT=<ID=ANRP,Number=1,Type=Integer,Description=""Count of read pairs at this breakend assembled into a contig that does not support the breakpoint."">"
"##FORMAT=<ID=ANRPQ,Number=1,Type=Float,Description=""Quality score of read pairs at this breakend assembled into a contig that does not support the breakpoint."">"
"##FORMAT=<ID=ANSR,Number=1,Type=Integer,Description=""Count of split reads at this breakend assembled into a contig that does not support the breakpoint."">"
"##FORMAT=<ID=ANSRQ,Number=1,Type=Float,Description=""Quality score of split reads at this breakend assembled into a contig that does not support the breakpoint."">"
"##FORMAT=<ID=ASQ,Number=1,Type=Float,Description=""Pro-rata quality score contribution of assemblies supporting breakpoint"">"
"##FORMAT=<ID=ASRP,Number=1,Type=Integer,Description=""Count of read pairs incorporated into any breakpoint assembly"">"
"##FORMAT=<ID=ASSR,Number=1,Type=Integer,Description=""Count of split, soft clipped or indel-containing reads incorporated into any breakpoint assemblies"">"
"##FORMAT=<ID=BAQ,Number=1,Type=Float,Description=""Pro-rata quality score contribution of assemblies supporting just local breakend"">"
"##FORMAT=<ID=BASRP,Number=1,Type=Integer,Description=""Count of read pairs incorporated into any breakend assembly"">"
"##FORMAT=<ID=BASSR,Number=1,Type=Integer,Description=""Count of split, soft clipped or indel-containing reads incorporated into any breakend assemblies"">"
"##FORMAT=<ID=BQ,Number=1,Type=Float,Description=""Quality score of breakend evidence after evidence reallocation"">"
"##FORMAT=<ID=BSC,Number=1,Type=Integer,Description=""Count of soft clips supporting just local breakend per category"">"
"##FORMAT=<ID=BSCQ,Number=1,Type=Float,Description=""Quality score of soft clips supporting just local breakend per category"">"
"##FORMAT=<ID=BUM,Number=1,Type=Integer,Description=""Count of read pairs (with one read unmapped) supporting just local breakend per category"">"
"##FORMAT=<ID=BUMQ,Number=1,Type=Float,Description=""Quality score of read pairs (with one read unmapped) supporting just local breakend per category"">"
"##FORMAT=<ID=BVF,Number=1,Type=Integer,Description=""Count of fragments providing breakend for the variant allele."">"
"##FORMAT=<ID=CASQ,Number=1,Type=Float,Description=""Pro-rata quality score of complex compound breakpoint assemblies supporting breakpoint from elsewhere"">"
"##FORMAT=<ID=GT,Number=1,Type=String,Description=""Genotype"">"
"##FORMAT=<ID=IC,Number=1,Type=Integer,Description=""Count of read indels supporting breakpoint per category"">"
"##FORMAT=<ID=IQ,Number=1,Type=Float,Description=""Quality score of read indels supporting breakpoint per category"">"
"##FORMAT=<ID=QUAL,Number=1,Type=Float,Description=""Quality score of breakend evidence after evidence reallocation"">"
"##FORMAT=<ID=RASQ,Number=1,Type=Float,Description=""Pro-rata quality score contribution of assemblies supporting breakpoint from remote breakend"">"
"##FORMAT=<ID=REF,Number=1,Type=Integer,Description=""Count of reads mapping across this breakend"">"
"##FORMAT=<ID=REFPAIR,Number=1,Type=Integer,Description=""Count of reference read pairs spanning this breakend supporting the reference allele"">"
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"##FORMAT=<ID=RPQ,Number=1,Type=Float,Description=""Quality score of read pairs supporting breakpoint per category"">"
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"##INFO=<ID=ANSRQ,Number=1,Type=Float,Description=""Quality score of split reads at this breakend assembled into a contig that does not support the breakpoint."">"
"##INFO=<ID=AS,Number=1,Type=Integer,Description=""Count of assemblies supporting breakpoint"">"
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"##INFO=<ID=BAQ,Number=1,Type=Float,Description=""Quality score of assemblies supporting just local breakend"">"
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"##INFO=<ID=CIPOS,Number=2,Type=Integer,Description=""Confidence interval around POS for imprecise variants"">"
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"##INFO=<ID=CQ,Number=1,Type=Float,Description=""Breakpoint quality score before evidence reallocation"">"
"##INFO=<ID=EVENT,Number=1,Type=String,Description=""ID of event associated to breakend"">"
"##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description=""Length of base pair identical micro-homology at event breakpoints"">"
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"##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description=""Imprecise structural variation"">"
"##INFO=<ID=INSRM,Number=.,Type=String,Description=""RepeatMasker classification of inserted sequence in the format of RepeatType#RepeatClass|repeat position|repeat orientation|insertion sequence CIGAR|repeat masker alignment score|edit distance to canonical repeat sequence. Edit distance may be blank."">"
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"##INFO=<ID=INSRMRC,Number=1,Type=String,Description=""Inserted sequence repeatmasker repeat class."">"
"##INFO=<ID=INSRMRO,Number=1,Type=String,Description=""Inserted sequence repeatmasker repeat orientation."">"
"##INFO=<ID=INSRMRT,Number=1,Type=String,Description=""Inserted sequence repeatmasker repeat type."">"
"##INFO=<ID=INSTAXID,Number=1,Type=Integer,Description=""NCBI Taxonomy identifier for inserted sequence."">"
"##INFO=<ID=IQ,Number=1,Type=Float,Description=""Quality score of read indels supporting breakpoint"">"
"##INFO=<ID=MATEID,Number=.,Type=String,Description=""ID of mate breakends"">"
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"##INFO=<ID=SELF,Number=0,Type=Flag,Description=""Indicates a breakpoint is self-intersecting"">"
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gridssVersion=2.13.2-gridss

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PLACEHOLDER.filter.deduped.recalibrated.bam.viral.bam

chr1 62267109 gridss0f_639b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:2545] 229.02 LOW_QUAL;NO_RP BEALN=chr1:62266990|-|120M|60;EVENT=gridss0f_639b;INSTAXID=9606;MATEID=gridss0f_639b_virus;SVTYPE=BND GT ./. chr1 109599181 gridss0b_340b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:1185[ 304.09 ASSEMBLY_BIAS;LOW_QUAL BEALN=chr1:109599104|+|78M|60;EVENT=gridss0b_340b;INSTAXID=9606;MATEID=gridss0b_340b_virus;SVTYPE=BND GT ./. chr1 158690478 gridss0f_395b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:1337]N 963.28 LOW_QUAL;NO_RP BEALN=chr1:158690478|+|91M|60;EVENT=gridss0f_395b;INSRM=AluSc8#SINE/Alu|192|-|91M|585|17;INSRMP=1.00;INSRMRC=SINE/Alu;INSRMRO=-;INSRMRT=AluSc8;INSTAXID=9606;MATEID=gridss0f_395b_virus;SVTYPE=BND GT ./. chr1 182907123 gridss0f_237b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:800] 116.26 LOW_QUAL BEALN=chr1:182906953|-|171M|60;EVENT=gridss0f_237b;INSRM=AluJb#SINE/Alu|2|+|8S163M|1019|30;INSRMP=0.953;INSRMRC=SINE/Alu;INSRMRO=+;INSRMRT=AluJb;INSTAXID=9606;MATEID=gridss0f_237b_virus;SVTYPE=BND GT ./. chr2 22354317 gridss0f_1479b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:6285]N 184.55 LOW_QUAL;NO_RP BEALN=chr2:22354317|+|116M|60;EVENT=gridss0f_1479b;INSTAXID=9606;MATEID=gridss0f_1479b_virus;SVTYPE=BND GT ./. chr2 45965709 gridss0f_1443b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:6211] 72.94 LOW_QUAL;NO_RP BEALN=chr2:45965668|-|42M|60;EVENT=gridss0f_1443b;INSTAXID=9606;MATEID=gridss0f_1443b_virus;SVTYPE=BND GT ./. chr2 73507540 gridss0b_983b_host N [adjusted_kraken_taxid_333760_NC_001526.4:4380[N 374.91 LOW_MAPQ;LOW_QUAL;NO_RP BEALN=chr2:73507540|-|79M|2;EVENT=gridss0b_983b;INSRM=L1P1#LINE/L1|3308|+|79M|633|1;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1P1;INSTAXID=9606;MATEID=gridss0b_983b_virus;SVTYPE=BND GT ./. chr2 81636600 gridss0f_42b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:203]N 80.24 LOW_QUAL;NO_RP BEALN=chr2:81636600|+|63M|60;EVENT=gridss0f_42b;INSRM=L1M1#LINE/L1|3409|+|63M|342|9;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1M1;INSTAXID=9606;MATEID=gridss0f_42b_virus;SVTYPE=BND GT ./. chr2 101871773 gridss0f_907b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:3628]N 266.99 LOW_QUAL;NO_RP BEALN=chr2:101871773|+|104M|60;EVENT=gridss0f_907b;INSTAXID=9606;MATEID=gridss0f_907b_virus;SVTYPE=BND GT ./. chr2 106208221 gridss0f_1704b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:7743] 169.66 LOW_QUAL BEALN=chr2:106208085|-|137M|60;EVENT=gridss0f_1704b;INSTAXID=9606;MATEID=gridss0f_1704b_virus;SVTYPE=BND GT ./. chr2 168824415 gridss0f_1402b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:6082]N 120.68 LOW_QUAL "BEALN=chr2:168824415|+|92M64S|10,chr22:36001874|-|64S92M|,chr14:67922808|+|99M57S|,chr8:116579414|-|64S82M10S|,chr14:63862834|+|85H71M|5;EVENT=gridss0f_1402b;INSRM=SVA_B#Retroposon/SVA|145|+|145M|552|39,AluSx#SINE/Alu|85|-|145S11M|790|1;INSRMP=0.929;INSRMRC=Retroposon/SVA;INSRMRO=+;INSRMRT=SVA_B;INSTAXID=9606;MATEID=gridss0f_1402b_virus;SVTYPE=BND" GT ./. chr2 191704749 gridss0b_934b_host N [adjusted_kraken_taxid_333760_NC_001526.4:4170[N 158.55 LOW_QUAL;NO_RP BEALN=chr2:191704749|-|95M|60;EVENT=gridss0b_934b;INSRM=MamRep564#Unknown|103|-|2S47M|231|9;INSRMP=0.495;INSRMRC=Unknown;INSRMRO=-;INSRMRT=MamRep564;INSTAXID=9606;MATEID=gridss0b_934b_virus;SVTYPE=BND GT ./. chr2 222376779 gridss0b_1211b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:5445[ 185.64 LOW_QUAL;NO_RP BEALN=chr2:222376729|+|51M|46;EVENT=gridss0b_1211b;INSRM=L1M1#LINE/L1|2953|+|51M|357|3;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1M1;INSTAXID=9606;MATEID=gridss0b_1211b_virus;SVTYPE=BND GT ./. chr3 33891771 gridss0f_608b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:2444] 555.72 LOW_QUAL;NO_RP BEALN=chr3:33891658|-|114M|60;EVENT=gridss0f_608b;INSRM=L1P5#LINE/L1|5509|+|114M|758|14;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1P5;INSTAXID=9606;MATEID=gridss0f_608b_virus;SVTYPE=BND GT ./. chr3 47451184 gridss0f_931b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:3815] 161.16 LOW_QUAL;NO_RP BEALN=chr3:47451133|-|52M|60;EVENT=gridss0f_931b;INSTAXID=9606;MATEID=gridss0f_931b_virus;SVTYPE=BND GT ./. chr3 65552018 gridss0f_153b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:503]N 360.52 LOW_QUAL BEALN=chr3:65552018|+|163M|60;EVENT=gridss0f_153b;INSTAXID=9606;MATEID=gridss0f_153b_virus;SVTYPE=BND GT ./. chr3 144787549 gridss0f_1503b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:6543]N 135.52 LOW_QUAL;NO_RP BEALN=chr3:144787549|+|92M|60;EVENT=gridss0f_1503b;INSRM=L1P3#LINE/L1|3780|-|92M|560|16;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=-;INSRMRT=L1P3;INSTAXID=9606;MATEID=gridss0f_1503b_virus;SVTYPE=BND GT ./. chr3 162403765 gridss0f_1456b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:6243] 234.14 LOW_QUAL;NO_RP BEALN=chr3:162403710|-|56M|60;EVENT=gridss0f_1456b;INSRM=HERV4_I#LTR/ERV1|2015|+|14S42M|341|2;INSRMP=0.750;INSRMRC=LTR/ERV1;INSRMRO=+;INSRMRT=HERV4_I;INSTAXID=9606;MATEID=gridss0f_1456b_virus;SVTYPE=BND GT ./. chr3 165408901 gridss0b_140b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:433[ 267.46 LOW_QUAL;NO_RP BEALN=chr3:165408796|+|106M|60;EVENT=gridss0b_140b;INSRM=L1PA5#LINE/L1|5939|+|106M|760|14;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1PA5;INSTAXID=9606;MATEID=gridss0b_140b_virus;SVTYPE=BND GT ./. chr3 177648218 gridss0f_824b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:3281]N 178.29 LOW_QUAL;NO_RP BEALN=chr3:177648218|+|78M|60;EVENT=gridss0f_824b;INSTAXID=9606;MATEID=gridss0f_824b_virus;SVTYPE=BND GT ./. chr4 23424468 gridss0f_651b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:2568] 199.19 LOW_QUAL BEALN=chr4:23424329|-|56M1I84M|60;EVENT=gridss0f_651b;INSRM=L2a#LINE/L2|3310|-|107M|410|33;INSRMP=0.759;INSRMRC=LINE/L2;INSRMRO=-;INSRMRT=L2a;INSTAXID=9606;MATEID=gridss0f_651b_virus;SVTYPE=BND GT ./. chr4 56421911 gridss0b_1346b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:6122[ 140.38 LOW_QUAL;NO_RP BEALN=chr4:56421835|+|77M|60;EVENT=gridss0b_1346b;INSTAXID=9606;MATEID=gridss0b_1346b_virus;SVTYPE=BND GT ./. chr4 96171553 gridss0f_1228b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:5111] 88.79 LOW_QUAL;NO_RP BEALN=chr4:96171453|-|101M|60;EVENT=gridss0f_1228b;INSTAXID=9606;MATEID=gridss0f_1228b_virus;SVTYPE=BND GT ./. chr4 117923313 gridss0b_354b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:1255[ 483.42 LOW_QUAL;NO_RP "BEALN=chr4:117923220|+|2S94M|15,chr11:105017528|+|4S92M|,chr11:10174385|+|6S90M|,chr7:23322297|+|8S88M|,chr22:28391542|-|87M9S|,chr4:90228843|+|4S92M|;EVENT=gridss0b_354b;INSRM=L1HS#LINE/L1|1232|+|96M|663|5;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1HS;INSTAXID=9606;MATEID=gridss0b_354b_virus;SVTYPE=BND" GT ./. chr4 148837082 gridss0f_86b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:355] 166.37 LOW_QUAL;NO_RP BEALN=chr4:148836995|-|88M|60;EVENT=gridss0f_86b;INSTAXID=9606;MATEID=gridss0f_86b_virus;SVTYPE=BND GT ./. chr4 184303594 gridss0b_797b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:3520[ 157.89 LOW_QUAL;NO_RP BEALN=chr4:184303514|+|81M|60;EVENT=gridss0b_797b;INSRM=L1M5#LINE/L1|2857|+|4S77M|381|14;INSRMP=0.951;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1M5;INSTAXID=9606;MATEID=gridss0b_797b_virus;SVTYPE=BND GT ./. chr5 27089054 gridss0f_1319b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:5676]N 140.75 LOW_QUAL;NO_RP BEALN=chr5:27089054|+|66M|43;EVENT=gridss0f_1319b;INSRM=Alu#SINE/Alu|221|-|1S65M|467|8;INSRMP=0.985;INSRMRC=SINE/Alu;INSRMRO=-;INSRMRT=Alu;INSTAXID=9606;MATEID=gridss0f_1319b_virus;SVTYPE=BND GT ./. chr5 49601602 gridss0b_460b_host N [adjusted_kraken_taxid_333760_NC_001526.4:1741[GGAATN 124.74 LOW_QUAL "BEALN=chr5:49601602|-|5S76M5S|26,chr20:31106782|-|86M|;EVENT=gridss0b_460b;INSTAXID=9606;MATEID=gridss0b_460b_virus;SVTYPE=BND" GT ./. chr5 60623311 gridss0b_191b_host N [adjusted_kraken_taxid_333760_NC_001526.4:531[N 280.08 ASSEMBLY_BIAS;LOW_QUAL;NO_RP BEALN=chr5:60623311|-|81M|60;EVENT=gridss0b_191b;INSRM=L1M4#LINE/L1|4767|+|33S48M|280|7;INSRMP=0.593;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1M4;INSTAXID=9606;MATEID=gridss0b_191b_virus;SVTYPE=BND GT ./. chr5 71531566 gridss0b_586b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:2526[ 245.1 ASSEMBLY_BIAS;LOW_MAPQ;LOW_QUAL;NO_RP "BEALN=chr5:71531527|+|40M|0,chr5_KI270897v1_alt:1061502|+|40M|,chr5_GL339449v2_alt:1530012|+|40M|;EVENT=gridss0b_586b;INSTAXID=9606;MATEID=gridss0b_586b_virus;SVTYPE=BND" GT ./. chr5 136668465 gridss0f_1155b_host N NAAA]adjusted_kraken_taxid_333760_NC_001526.4:4764] 493.19 LOW_QUAL;NO_RP BEALN=chr5:136668364|-|102M3S|60;EVENT=gridss0f_1155b;INSRM=L1M2#LINE/L1|3095|-|3S102M|409|17;INSRMP=0.971;INSRMRC=LINE/L1;INSRMRO=-;INSRMRT=L1M2;INSTAXID=9606;MATEID=gridss0f_1155b_virus;SVTYPE=BND GT ./. chr5 142989499 gridss0b_759b_host N [adjusted_kraken_taxid_333760_NC_001526.4:3365[GN 141.83 LOW_MAPQ;LOW_QUAL;NO_RP "BEALN=chr5:142989499|-|1S38M|9,chr4:100047552|-|3S36M|;EVENT=gridss0b_759b;INSRM=L1P2#LINE/L1|2106|+|39M|302|1;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1P2;INSTAXID=9606;MATEID=gridss0b_759b_virus;SVTYPE=BND" GT ./. chr6 13708882 gridss0b_18b_host N NGAAAAAAAAA[adjusted_kraken_taxid_333760_NC_001526.4:86[ 611.32 LOW_QUAL BEALN=chr6:13708823|+|60M10S|60;EVENT=gridss0b_18b;INSTAXID=9606;MATEID=gridss0b_18b_virus;SVTYPE=BND GT ./. chr6 55110284 gridss0f_1466b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:6259]N 601.87 LOW_QUAL BEALN=chr6:55110284|+|208M|60;EVENT=gridss0f_1466b;INSRM=L1PBa#LINE/L1|2769|+|208M|1171|29;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=+;INSRMRT=L1PBa;INSTAXID=9606;MATEID=gridss0f_1466b_virus;SVTYPE=BND GT ./. chr6 59535318 gridss0f_343b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:1209] 369.04 LOW_MAPQ;LOW_QUAL;NO_RP BEALN=chr6:59535254|-|65M|0;EVENT=gridss0f_343b;INSRM=ALR/Alpha#Satellite/centr|78|-|65M|460|7;INSRMP=1.00;INSRMRC=Satellite/centr;INSRMRO=-;INSRMRT=ALR/Alpha;INSTAXID=9606;MATEID=gridss0f_343b_virus;SVTYPE=BND GT ./. chr6 105488572 gridss0b_454b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:1705[ 261.85 LOW_QUAL;NO_RP BEALN=chr6:105488463|+|110M|60;EVENT=gridss0b_454b;INSTAXID=9606;MATEID=gridss0b_454b_virus;SVTYPE=BND GT ./. chr6 170695037 gridss0b_272b_host N [adjusted_kraken_taxid_333760_NC_001526.4:876[N 432.99 LOW_MAPQ;LOW_QUAL BEALN=chr6:170695037|-|122M|0;EVENT=gridss0b_272b;INSTAXID=9606;MATEID=gridss0b_272b_virus;SVTYPE=BND GT ./. chr7 26995314 gridss0b_864b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:3843[ 73.33 LOW_QUAL BEALN=chr7:26995174|+|141M|60;EVENT=gridss0b_864b;INSTAXID=9606;MATEID=gridss0b_864b_virus;SVTYPE=BND GT ./. chr7 68482636 gridss0f_161b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:513] 193.1 LOW_QUAL;NO_RP BEALN=chr7:68482549|-|88M|60;EVENT=gridss0f_161b;INSRM=THE1B#LTR/ERVL-MaLR|289|-|12S76M|633|4;INSRMP=0.864;INSRMRC=LTR/ERVL-MaLR;INSRMRO=-;INSRMRT=THE1B;INSTAXID=9606;MATEID=gridss0f_161b_virus;SVTYPE=BND GT ./. chr7 81565016 gridss0b_286b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:930[ 110.92 LOW_QUAL;NO_RP BEALN=chr7:81564968|+|49M|60;EVENT=gridss0b_286b;INSTAXID=9606;MATEID=gridss0b_286b_virus;SVTYPE=BND GT ./. chr8 28626436 gridss0b_1009b_host N [adjusted_kraken_taxid_333760_NC_001526.4:4434[N 470.26 LOW_QUAL;NO_RP BEALN=chr8:28626436|-|113M|60;EVENT=gridss0b_1009b;INSTAXID=9606;MATEID=gridss0b_1009b_virus;SVTYPE=BND GT ./. chr8 51798524 gridss0f_747b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:2915] 113.07 LOW_QUAL;NO_RP BEALN=chr8:51798479|-|46M|60;EVENT=gridss0f_747b;INSRM=L1PREC2#LINE/L1|5287|-|46M|263|5;INSRMP=1.00;INSRMRC=LINE/L1;INSRMRO=-;INSRMRT=L1PREC2;INSTAXID=9606;MATEID=gridss0f_747b_virus;SVTYPE=BND GT ./. chr8 75771324 gridss0b_1047b_host N [adjusted_kraken_taxid_333760_NC_001526.4:4563[N 420.21 LOW_QUAL BEALN=chr8:75771324|-|129M|60;EVENT=gridss0b_1047b;INSTAXID=9606;MATEID=gridss0b_1047b_virus;SVTYPE=BND GT ./. chr8 81872211 gridss0f_384b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:1312] 279.48 LOW_QUAL;NO_RP BEALN=chr8:81872155|-|1S57M|60;EVENT=gridss0f_384b;INSTAXID=9606;MATEID=gridss0f_384b_virus;SVTYPE=BND GT ./. chr8 125434880 gridss0f_540b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:2171]N 184.56 LOW_QUAL BEALN=chr8:125434880|+|47M1I65M|60;EVENT=gridss0f_540b;INSTAXID=9606;MATEID=gridss0f_540b_virus;SVTYPE=BND GT ./. chr9 10531278 gridss0f_175b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:528]N 280.7 LOW_QUAL;NO_RP BEALN=chr9:10531278|+|67M|60;EVENT=gridss0f_175b;INSTAXID=9606;MATEID=gridss0f_175b_virus;SVTYPE=BND GT ./. chr9 27771173 gridss0b_1230b_host N [adjusted_kraken_taxid_333760_NC_001526.4:5601[N 517.29 LOW_QUAL;NO_RP BEALN=chr9:27771173|-|127M|60;EVENT=gridss0b_1230b;INSRM=MER41B#LTR/ERV1|525|-|22S105M|788|14;INSRMP=0.827;INSRMRC=LTR/ERV1;INSRMRO=-;INSRMRT=MER41B;INSTAXID=9606;MATEID=gridss0b_1230b_virus;SVTYPE=BND GT ./. chr9 31177351 gridss0b_1290b_host N [adjusted_kraken_taxid_333760_NC_001526.4:5896[N 91.78 LOW_QUAL;NO_RP BEALN=chr9:31177351|-|55M|60;EVENT=gridss0b_1290b;INSTAXID=9606;MATEID=gridss0b_1290b_virus;SVTYPE=BND GT ./. chr9 101580545 gridss0b_1080b_host N N[adjusted_kraken_taxid_333760_NC_001526.4:4781[ 2143.3 ASSEMBLY_BIAS BEALN=chr9:101580402|+|144M|60;EVENT=gridss0b_1080b;INSTAXID=9606;MATEID=gridss0b_1080b_virus;SVTYPE=BND GT ./. chr9 117351554 gridss0b_1446b_host N [adjusted_kraken_taxid_333760_NC_001526.4:6557[N 179.82 LOW_QUAL BEALN=chr9:117351554|-|179M|60;EVENT=gridss0b_1446b;INSTAXID=9606;MATEID=gridss0b_1446b_virus;SVTYPE=BND GT ./. chr9 119391510 gridss0f_1409b_host N N]adjusted_kraken_taxid_333760_NC_001526.4:6097] 94.51 LOW_QUAL;NO_RP BEALN=chr9:119391417|-|94M|60;EVENT=gridss0f_1409b;INSTAXID=9606;MATEID=gridss0f_1409b_virus;SVTYPE=BND GT ./. chr10 53498922 gridss0f_1349b_host N ]adjusted_kraken_taxid_333760_NC_001526.4:5858

AqsaAlam commented 6 months ago

Hi,

Ah, I just realized the problem! I think the sample had run multiple times. I found the other version of the vcf with 57 lines in the VCF file, and another summary.tsv with integrations = 92.

You can consider my question solved!

Cheers,

Aqsa Alam

From: Aqsa Alam Sent: Thursday, April 18, 2024 11:14 AM To: PapenfussLab/gridss @.***> Subject: RE: [PapenfussLab/gridss] Difference in number of integrations in virus summary vs. VCF (Issue #658)

Hi!

Thanks for your quick response!

The vcf summary output says "integrations = 57" (I've attached the file). The vcf file has 184 entries, 92 of which are human chromosome breakpoints. (I've also attached the file).

I've confirmed they are the same sample.

Cheers,

Aqsa Alam

From: Daniel Cameron @.**@.>> Sent: Wednesday, April 17, 2024 11:02 PM To: PapenfussLab/gridss @.**@.>> Cc: Aqsa Alam @.**@.>>; Author @.**@.>> Subject: Re: [PapenfussLab/gridss] Difference in number of integrations in virus summary vs. VCF (Issue #658)

How are you counting the 57 vs 92? A single integration site can have 2 breakpoints (left and right size of the insertion in human coordinate space) which is 4 VCF BND records.

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