Extract cis and trans mutations from bam file

Question

[RD]

Hi All,

I have annotated SNPs from a VCF file, and at position 110294564, there is a primary mutation, let's call it P260R. I want to extract all reads containing the P260R mutation and then annotate those reads to identify other mutations on the same read, essentially finding cis mutations associated with P260R. How can I perform this extraction and annotation process.

Here is the IGV screenshot.

Thanks in advance!

[GenoMax]

Extracting reads:How to extract reads with a known variant form a bam file and then perhaps this: How to extract read counts at the mutation locations