intersect snp and exon coordinates

Question

[fabbri.marco]

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

Answer 1

[GouthamAtla]

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.

[Brian Bushnell]

Great answer! I've linked bedtools