vcfm2acf deal for vcf file about glactools HOT 15 CLOSED

from glactools.

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

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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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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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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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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

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

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

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

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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.

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