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intersect snp and exon coordinates

I intersected exon coordinates with coordinates of mutations and I get the bed file with exons that contain mutations. This can be done with bedtools. I would like to do a little bit more articulates, I would like to do the same but select only exons that intersect with two mutations. Any suggestion? Tank you

Marco

snp sequence
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updated by GouthamAtla GouthamAtla • written by fabbri.marco • fabbri.marco

1 answer

exons.bed

chr1    100 200
chr1    300 800

SNP.bed or a VCF

chr1    150 151
chr1    301 302
chr1    501 502
chr1    900 901

.

% intersectBed -a SNP.bed -b exon.bed -wb
chr1    150 151 chr1    100 200
chr1    301 302 chr1    300 800
chr1    501 502 chr1    300 800

The columns 4,5,6 tells how many times an exon carries a SNP. so just uniq -c or clusterBed/groupBy will help to get the exact counts.

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written by GouthamAtla GouthamAtla

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