How to determine the number of SNPs captured by a list of genes in VCF file
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8.5 years ago
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I have a bed file called mybedfile.bed which has a defined region for a list of genes. I have VCF files split into 24 chromosomes. I want to determine the number of SNPs captured by the regions defined in mybedfile.bed. What would be the easiest way to get this done (preferably in R)?

SNPs • 1.3k views
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Why not bedtools intersect?

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