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arq5x / bedtools

A powerful toolset for genome arithmetic.
http://code.google.com/p/bedtools/
GNU General Public License v2.0
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Request: Add minimum mapping quality to genomecov #117

Closed tantrev closed 8 years ago

tantrev commented 8 years ago

Pretty simple, would just be nice if minimum mapping quality could be specified in genomecov.

arq5x commented 8 years ago

The prefered method for this would be to use samtools to do the filtering (e.g., only compute coverage for reads with MAPQ>=20):

samtools view -q 20 -u aln.bam | bedtools genomecov -ibam - > cov.q20.out