Extracting variant reads and reference reads quickly from mapped files

Question

[graeme.thorn]

As per the question, I want to check whether the effect seen here in this paper: https://www.ncbi.nlm.nih.gov/pubmed/30404863 is true for my samples (the effect that fragments of cfDNA containing tumour-specific variants are shorter than those that don't, indicating the tumouric origin of those fractions)

I have a list of candidate variants to check in vcf format, so I can extract all the mapped reads that cover the variant locations using bedtools or similar, but these will contain both those that have the variant and those that don't.

Is there a quick way of subsetting these reads to split into variant/reference?

Answer 1

[Pierre Lindenbaum]

related ? Extract PE Reads (with their mates) supporting variants in vcf file