Hi all, I have bam files from which I would like to extract 1 specific column (ie chr:position). I won't to have all alleles, even if they come from low quality reads. And even if the position is not a SNP (ie all alleles are the same or almost).
I tried to use "samtools view" giving the position but then the output is all reads that overlap the position so it's not exactly what I am looking for.
Does anyone has any idea how I could solve my problem ?
Thanks a lot. M.D