Allele count from BAM file

Question

[mona11224]

How to get reference and alternate allele count from BAM file at a given chromosomal position?

Answer 1

[GouthamAtla]

ASEReadCounter

[mona11224]

I dont have VCF file have only .bam file and in that file chromosomal position is specified EX: chr12:6789007

[GouthamAtla]

If you have reference genome, generate a VCF file from your positions of interest or call SNPs from your bam file and then calculate allele counts.

Answer 2

[Gabriel R.]

It is one line in glactools:

glactools  bam2acf [reference].fa [iinput].bam  sampleid  |  glactools  view - |cut -f 1-3,6

In the last column, the format is REF,ALT:cpg

Be aware that it filters out reads marked as QC failed and PCR duplicates.