Question: Calculate Allele balance by sample
1
gravatar for kirannbishwa01
3.6 years ago by
kirannbishwa011.1k
United States
kirannbishwa011.1k wrote:

I have a VCF file which variants called and has several field like AD, DP, AF, AC, etc. I however also need to calculate the AB (allele balance for each sample) which the information available in this vcf file. I tried looking for a softwae online but I couldn't find any.

Here is a sample output of the vcf file:

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1

X 5867701 . T C,G 231.77 . AC=1,1;AF=0.500,0.500;AN=2;DP=8;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=45.48;QD=28.97;SOR=1.179 GT:AD:DP:GQ:PL 1/2:0,4,4:8:96:260,167,153,96,0,151

X 7753630 . A T,C 469.77 . AC=1,1;AF=0.500,0.500;AN=2;DP=13;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;QD=30.18;SOR=2.833 GT:AD:DP:GQ:PL 1/2:0,10,3:13:88:498,88,96,416,0,407

Thanks in advance.

rna-seq snp allele balance • 1.7k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by kirannbishwa011.1k
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