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bedtools intersect

Intersect multiple files

As of version 2.21.0, bedtools is able to intersect an “A” file against one or more “B” files. This greatly simplifies analyses involving multiple datasets relevant to a given experiment. For example, let’s intersect exons with CpG islands, GWAS SNPs, an the ChromHMM annotations:

bedtools intersect -a exons.bed -b cpg.bed gwas.bed hesc.chromHmm.bed -sorted | head

Now by default, this isn’t incredibly informative as we can’t tell which of the three “B” files yielded the intersection with each exon. However, if we use the -wa and wb options, we can see from which file number (following the order of the files given on the command line) the intersection came. In this case, the 7th column reflects this file number:

bedtools intersect -a exons.bed -b cpg.bed gwas.bed hesc.chromHmm.bed -sorted -wa -wb \
   | head -n 10000 \
   | tail -n 10

Additionally, one can use file “labels” instead of file numbers to facilitate interpretation, especially when there are many files involved:

bedtools intersect -a exons.bed -b cpg.bed gwas.bed hesc.chromHmm.bed -sorted -wa -wb -names cpg gwas chromhmm \
   | head -n 10000 \
   | tail -n 10
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