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Generate A Subset Of Bam Or Reads Based On Vcf

Generate a subset of BAM or reads based on VCF

After mapping, I am interested in extracting a subset of bam or reads with certain genoytpes. Could you please advise me some efficient ways to do this?

Thanks in advance!

vcf bam
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updated by Ram Ram • written by jlduan • jlduan

2 answers

loop over each mutation and extract the subset of BAM using samtools view in.bam chr:start-end

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written by Pierre Lindenbaum Pierre Lindenbaum

If two different genotypes are in the same positon, this method cannot distinguish them.

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written by jlduan • jlduan

Via BEDOPS and bash substitution:

$ bedops -e 1 <(bam2bed < reads.bam) <(vcf2bed < variants.vcf) > reads_overlapping_variants.bed
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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

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