Experiment with minBaseQualityScore in Mutect

broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead

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Experiment with minBaseQualityScore in Mutect #1113

Closed davidbenjamin closed 7 years ago

davidbenjamin commented 7 years ago

This sets the minimum base quality to consider a base in the assembly graph. By default it's 10, but in practice anything under 20 is usually junk. We could probably get a performance boost just by running Mutect with a higher value than the default.

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #3023 via ZenHub