Finding heterozygous sites in a BAM file
Can someone guide me on how we can find heterozygous sites given a germline BAM file? (preferably in R)
Basically, I would like to know the heterozygous sites in the germline BAM and then, using the reads data from the tumor BAM file, look for those reads containing both a heterozygous location and a mutation.
Thanks
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Maybe I'm misunderstanding something but... you are interested in doing something like variant calling and then extract heterozygous variants?
Yes, you are right. Sorry for my very-basic dna-seq vocabulary. I have Mutect-inferred variant calling data for the tumor. I also have allele-specific copy number data (using ASCAT) for the same.
If I understand correctly, you are trying to - "find true somatic mutations at germline heterozygous sites". Most somatic variant callers like MuTect should handle this exception correctly. If you explain the biological question you're trying to answer, then we can point you the right way.