vcfm2acf deal for vcf file

[HengLiang1993]

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]

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 <#30>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQRNI6X27SW75EDHVC6N63VV7BQTANCNFSM54VQSY2A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[HengLiang1993]

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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[grenaud]

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

[HengLiang1993]

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]

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. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[HengLiang1993]

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]

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？ — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[HengLiang1993]

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]

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 — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQRNI7D54Y2MFWQD6UWFO3VWN36TANCNFSM54VQSY2A> . You are receiving this because you commented.Message ID: ***@***.***>

[grenaud]

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 — Reply to this email directly, view it on GitHub <#30 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAQRNI2D6GUOG2QKAWGOBMTVWPM2TANCNFSM54VQSY2A> . You are receiving this because you commented.Message ID: ***@***.***>

[HengLiang1993]

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]

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

[HengLiang1993]

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

[grenaud]

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

[HengLiang1993]

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.