Question: Calculate Allele balance by sample
0
gravatar for kirannbishwa01
2.4 years ago by
United States
kirannbishwa01830 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 • 1.2k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by kirannbishwa01830
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 476 users visited in the last hour