Extract allelic depths in a BAM
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5 months ago

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!

bam VCF • 335 views
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