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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Coverage not correct #49

Open parlundin opened 9 years ago

parlundin commented 9 years ago

Seems like qualimap wrongly use the duplicates when calculating coverage.

ewels commented 9 years ago

Qualimap issues page: https://bitbucket.org/kokonech/qualimap/issues?status=new&status=open

johandahlberg commented 9 years ago

I've submitted a feature request on this now: https://groups.google.com/forum/#!topic/qualimap/xQlXwuJl2r0

b97pla commented 8 years ago

new version still doesn't support excluding only the Picard-marked duplicates, a new feature request has been made: https://bitbucket.org/kokonech/qualimap/issues/26/bam-qc-add-an-option-to-control-skip