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grenaud / glactools

command-line tools for the management of genotype likelihoods and allele counts
http://grenaud.github.io/glactools/
GNU General Public License v3.0
29 stars 2 forks source link

vcfm2acf deal for vcf file #30

Closed HengLiang1993 closed 2 years ago

HengLiang1993 commented 2 years ago

Hello.

I have a problem using vcfm2acf.

glactools vcfm2acf --onlyGT --fai 1-12.fai sorted.output.vcf

error message: SimpleVCF: for line -18.3084 0 -12.4722 -19.8136 -14.5794 -34.0463 -19.8136 -14.5794 -34.0463 -34.0463 -19.8136 -14.5794 -34.0463 -34.0463 -34.0463 the GL field does not have 3 or 6 fields

The VCF file is form Freebayes, filtered with vbcftools.

Thanks.

Heng

grenaud commented 2 years ago

Hi Heng, Can you post the line that triggered this please? Could you also post 3 lines before and 3 lines after?

Gabriel

On Tue, Jul 26, 2022 at 1:10 PM HengLiang1993 @.***> wrote:

Hello.

I have a problem using vcfm2acf.

glactools vcfm2acf --onlyGT --fai 1-12.fai sorted.output.vcf

error message: SimpleVCF: for line -18.3084 0 -12.4722 -19.8136 -14.5794 -34.0463 -19.8136 -14.5794 -34.0463 -34.0463 -19.8136 -14.5794 -34.0463 -34.0463 -34.0463 the GL field does not have 3 or 6 fields

The VCF file is form Freebayes, filtered with vbcftools.

Thanks.

Heng

— Reply to this email directly, view it on GitHub https://github.com/grenaud/glactools/issues/30, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAQRNI6X27SW75EDHVC6N63VV7BQTANCNFSM54VQSY2A . You are receiving this because you are subscribed to this thread.Message ID: @.***>

HengLiang1993 commented 2 years ago

Hi It is the first one in my VCF file. And I post the line and 3 lines after : 1 315639 . A C 28428.3 . AB=0.304348;ABP=10.6577;AC=152;AF=0.475369;AN=308;AO=7;CIGAR=4M1X3M1X;DP=2065;DPB=2081.67;DPRA=1.13129;EPP=10.7656;EPPR=789.272;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=203;NUMALT=4;ODDS=0;PAIRED=1;PAIREDR=1;PAO=8.5;PQA=242.833;PQR=183.567;PRO=6.03333;QA=237;QR=32626;RO=863;RPL=5;RPP=5.80219;RPPR=834.926;RPR=2;RUN=1;SAF=4;SAP=3.32051;SAR=3;SRF=843;SRP=1707.3;SRR=20;TYPE=snp;technology.ILLUMINA=0.857143 GT:DP:AD:RO:QR:AO:QA:GL 0|1:12:5,7,0,0,0:5:175:7,0,0,0:240,0,0,0:-18.3084,0,-12.4722,-19.8136,-14.5794,-34.0463,-19.8136,-14.5794,-34.0463,-34.0463,-19.8136,-14.5794,-34.0463,-34.0463,-34.0463 0|1:7:1,6,0,0,0:1:26:6,0,0,0:238,0,0,0:-19.6856,0,-0.492618,-19.9866,-2.2988,-22.0059,-19.9866,-2.2988,-22.0059,-22.0059,-19.9866,-2.2988,-22.0059,-22.0059,-22.0059 0|1:6:1,5,0,0,0:1:41:5,0,0,0:201,0,0,0:-16.6638,0,-2.28839,-16.9649,-3.79354,-20.3503,-16.9649,-3.79354,-20.3503,-20.3503,-16.9649,-3.79354,-20.3503,-20.3503,-20.3503 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315681 . T C 40762.8 . 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grenaud commented 2 years ago

I am confused why there are 16 fields for GL, there should be tops 10 genotypes. What do they represent?

HengLiang1993 commented 2 years ago

Hi I am also confused. In the filter step, I used the code: vcfallelicprimitives -k -g capture_variants.vcf, I don't know if this is the cause.

grenaud commented 2 years ago

can you check in the original calls? And maybe check the manual?

On Wed, Jul 27, 2022 at 12:52 PM HengLiang1993 @.***> wrote:

Hi I am also confused. In the filter step, I used the code: vcfallelicprimitives -k -g capture_variants.vcf, I don't know if this is the cause.

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HengLiang1993 commented 2 years ago

HI in the https://samtools.github.io/hts-specs/VCFv4.2.pdf, GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc. For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats) I'm not sure if that explains why it has 16 fields for GL？

grenaud commented 2 years ago

yes I know but why would you have 16 fields unless you distinguish between AB and BA?

On Wed, Jul 27, 2022 at 1:03 PM HengLiang1993 @.***> wrote:

HI in the https://samtools.github.io/hts-specs/VCFv4.2.pdf, GL : genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields. In presence of the GT field the same ploidy is expected and the canonical order is used; without GT field, diploidy is assumed. If A is the allele in REF and B,C,... are the alleles as ordered in ALT, the ordering of genotypes for the likelihoods is given by: F(j/k) = (k*(k+1)/2)+j. In other words, for biallelic sites the ordering is: AA,AB,BB; for triallelic sites the ordering is: AA,AB,BB,AC,BC,CC, etc. For example: GT:GL 0/1:-323.03,-99.29,-802.53 (Floats) I'm not sure if that explains why it has 16 fields for GL？

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HengLiang1993 commented 2 years ago

Hi

Sorry for thr late reply. I have no idea. I see the GL has existed in the calling data. So I ask the maintainers of freebayes in yesterday but still no reply. If it is as you say(between AB and BA), and how can I do with the data in using vcfm2acf?

Best

Heng

grenaud commented 2 years ago

Well I would make sure that we understand what these 16 values mean. However, I would recommend using the option --onlyGT for now which only uses the GT field. Can you write a small script to remove the last 12 values of the GL field?

On Fri, Jul 29, 2022 at 8:38 AM HengLiang1993 @.***> wrote:

Hi

Sorry for thr late reply. I have no idea. I see the GL has existed in the calling data. So I ask the maintainers of freebayes in yesterday but still no reply. If it is as you say(between AB and BA), and how can I do with the data in using vcfm2acf?

Best

Heng

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grenaud commented 2 years ago

Well that is more a general python question than pop gen, can anyone who speaks python help you?

On Fri, Jul 29, 2022 at 3:35 PM HengLiang1993 @.***> wrote:

Hi

Thank you for your reply. So sorry, I'm a beginner in population genetiics and won't write write a small script to remove the last 12 values of the GL field. Can you help me?

Best

Heng

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HengLiang1993 commented 2 years ago

Hi

Thank you for your reply. So sorry, I'm a beginner in population genetiics and won't write write a small script to remove the last 12 values of the GL field. Can you give me a hand？

Best

Heng

grenaud commented 2 years ago

Well that is more a general python question than pop gen, can anyone who speaks python help you?

HengLiang1993 commented 2 years ago

Thank you for your kind help. But no one in my office currently can speaks python well.

grenaud commented 2 years ago

Ok I would hold off on making any changes in a code until we figure out what these values mean

HengLiang1993 commented 2 years ago

HI I used bcftools annotate -x 'FORMAT/GL' sorted.output.vcf > output.vcf to process the GL, and now it can be input file in vcfm2acf.