I have 45 pool-seq samples and aligned to reference (bam file). Those 45 pool-seq belong to 3 groups, say group 1, group 2 and group 3, thus each group have 15 samples. I combined 45 pool-seq samples and change the RGSM to Group number, ran freebayes to detect SNP. The vcf gives the result of genotype for each group, but not for each sample.
Now with given SNP information (chr and pos), I have to detect read count number supporting for each SNP in each pool-seq samples instead of group.
Given variant at chr1:2000, major allele is A and minor is G. I want to know how many A and how many G in pool-seq Sample_1 respectively at that position.
Any tools can do that?