bamutils / extract

Extracts reads based on regions in a BED file

Given a BAM file and a BED file, this script will extract only reads that
map to the given BED regions.

Specifically, if a read starts or ends within a BED region, it is extracted.
However, if a read completely spans a region (starting before and ending
after), it is ignored. If the read "touches" the region at all, it is

This tends to be faster than running 'bamutils filter' because this extracts
reads from a region, without iterating over all of the reads in the BAM file.
But, if you are already filtering the BAM file for other criteria, it is
probably worth it to just to the filtering with your other criteria.

Usage: bamutils extract {opts} in.bam out.bam regions.bed

  -ns    Ignore strandedness of reads and regions