Extract allelic depths in a BAM

Question

[mikothebichon]

Suppose that we already have a set of SNPs called in a matched normal bam file, is there a way to extract the allelic depths in a tumour bam in the form of VCF without running variant calling in both bams?

I understand that this is probably not the best practice, but I think it could be useful in situations where the tumour samples are sequenced at very low coverage. Thanks!

[German.M.Demidov]

Hi, for example https://github.com/sstadick/perbase can do it for you

In ngs-bits it is https://github.com/imgag/ngs-bits/blob/master/src/VariantAnnotateFrequency/main.cpp

[mikothebichon]

Thank you!