you can make it faster with grep -wFf qnames.list reads.sam On Mon, Aug 18, 2014 at 8:32 AM, csoeder <charles.soe...@gmail.com> wrote: > Hi! I would like to query a sam/bam file by its qname field. Can this be done > with samtools? I haven't seen anything like it in the documentation. I've > tried > > grep -f qnames.list reads.sam > output.out > > but it's unworkably slow. > > Thanks! > Charlie > > > ------------------------------------------------------------------------------ > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help
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