I am calling variants from a human sample using bwa mem to align the reads and gatk to call the variants. I'm trying to understand why a specific variant was not called in my sample. I have checked the bam alignments in a GUI viewer and I can see that there are reads supporting the missing variant. It looks like the issue is a low allelic balance, with far more reads supporting the reference than the alternate allele but I want to get the actual numbers.
So, given a specific variant like this:
chr22 425236 C T
How can I count the number of reads in my
sample.bam file that support that variant and the number that don't on Linux?