I have a VCF file and I got a little confused. I just need a small clarification.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Control Subject 10 15936159 . C T,<*> 0 . DP=123;ADF=54,9,0;ADR=52,8,0;AD=106,17,0;SCR=64;I16=54,52,9,8,3980,243762,675,52205,1714,69200,412,16468,2281,54527,423,10529;QS=1.78256,0.217441,0;VDB=0.0414177;SGB=-7.17793;RPB=0.011324;MQB=0.0522971;MQSB=0.278527;BQB=0.987088;MQ0F=0.520325 PL:DP:SP:ADF:ADR:AD:SCR:QS 0,48,255,66,255,255:24:0:15,1,0:7,1,0:22,2,0:3:724,8,0 0,22,145,253,190,248:99:1:39,8,0:45,7,0:84,15,0:61:926,241,0
Kindly please confirm whether my below-mentioned assumptions are valid considering the above information from the VCF file.
- Total number of reads at this position is 123 (Control 24 reads and Subject 99 reads).
- For 'Control' out of 24 reads, 22 reads assigned for the reference allele (C) and 2 reads assigned to alternate allele (T).
- For 'Subject' out of 99 reads, 84 reads assigned for the reference allele (C) and 15 reads assigned to alternate allele (T).
Also, one more question. Is there any easy way to add proportion/fraction/percentage of reads assigned to reference and alternate alleles for 'Control' and 'Subject' per SNP? or do I have to create a custom script for that?
Update: I found a solution for question 2 using bcftools. Here it is.
bcftools plugin fill-tags myVCF.vcf -- -t "FORMAT/VAF" > myVCF_allele_proportion.vcf