Clarification regarding VCF fields (file format)

Question

[EagleEye]

Hello everyone,

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

1. 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).

2. 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

Thank you.

[Arsenal]

Can you please share what is the version of given file, and maybe the full file. Have you read VCF version xx manual?

Answer 1

[atorreso]

Total number of reads at this position is 123 (Control 24 reads and Subject 99 reads).

Yes, this is the correct interpretation.

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).

This is also correct!

[EagleEye]

Thanks for your clarification.