gravatar for george.wiggins

2 hours ago by

New Zealand

This seems like a very simple task to do and I'd assume that samtools view would be able to do this. Basically all I want to do is to return all reads that a entirely contained within a given region.

samtools view bamfile "chr1:100-1000" returns any read the overlaps that region. For example a read may start before 100 or extend beyond 1000. I only what those that map entirely inside that region.



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