Hi! I'm trying to get the allele count for some snps in my bam files.
The variant calling was done by haplotypeCaller. The allele count in the output doesn't represent the real number of reads I have in my bam file, whitch is what I want.
I tried with bcftools mpileup, but the output only shows genotype liklyhoods. Also tried bam-readcount but it deosn't work with peired-end reads (I think).
I need to know the number of reads supports each allele in my vcf file.
Does anyone know how I coud do it?