Perhaps my Google-fu is failing me, because this doesn't seem like an uncommon need, but I can't find any answer here.
Say I have a SAM/BAM file, and a variant at a known location. I'd like to extract all the alignments from the BAM file which contain that variant. That is, I'd like the ALT, not the REF allele. I do not want all the reads at that location. Is there an existing tool or workflow out there that can accomplish this?
I would honestly be surprised if there wasn't, since I would imagine it's a common situation to be interested in a certain variant and investigate the reads supporting it. Specifically, I'd like to make sure there's no bias in where along the read it falls, or the strand of the read. I should note that my coverage is very high, so it's not feasible to extract all the reads covering the site and manually sort them out.
I've already started a script that does this by parsing CIGAR strings, but I wanted to check that it doesn't already exist before going further down this road.