How to interpret AC/RC fields in VCF files for a single sample

Question

[USA_225478]

Hi everyone,

I have received separate VCF files for multiple samples. I merged each sample into a single VCF file for each chromosome, and then sorted the resulting files using:

bcftools merge -l ID_list.txt -r $chrom -O z -o ${chrom}_merged.vcf.gz
bcftools sort ${chrom}_merged.vcf.gz -O z -o ${output}/${chrom}_sorted.vcf.gz

I've pasted a subset of the merged file (before filtering) for two samples below:

chr30   3962    .       AC      A       .       PASS    .       GT:RC:AC:GP:DS  0/0:0:0:1,1e-10,1e-10:3e-10     0/0:0:0:1,1e-10,1e-10:3e-10     
chr30   4015    .       TG      T       .       LOWCONF .       GT:RC:AC:GP:DS  0/0:0:0:1,1e-10,1e-10:3e-10     0/0:0:0:1,1e-10,1e-10:3e-10     
chr30   4026    .       T       G       .       PASS    .       GT:RC:AC:GP:DS  0/0:10:0:1,1e-10,1e-10:3e-10    0/0:2:0:1,1e-10,1e-10:3e-10     
chr30   4034    .       T       G       .       PASS    .       GT:RC:AC:GP:DS  0/0:9:0:1,1e-10,1e-10:3e-10     0/0:3:0:1,1e-10,1e-10:3e-10    
chr30   4070    .       G       A       .       PASS    .       GT:RC:AC:GP:DS  0/0:11:0:1,1e-10,1e-10:3e-10    0/0:3:0:1,1e-10,1e-10:3e-10     
chr30   4081    .       A       C       .       PASS    .       GT:RC:AC:GP:DS  0/0:8:0:1,1e-10,1e-10:3e-10     0/0:3:0:1,1e-10,1e-10:3e-10     

I understand that RC and AC are the allele counts for the REF and ALT alleles, respectively.

My questions are:

1) How do I interpret the RC/AC fields for a single individual? E.g. what does it mean for one sample to have an RC of 11?

2) Have I used an appropriate method of merging these files?

3) Is it possible to calculate MAF for each SNP using this file format?

Any help would be much appreciated!