Account for base qualities in M2 isActive

broadinstitute / gatk-protected

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

BSD 3-Clause "New" or "Revised" License

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Account for base qualities in M2 isActive #1089

Closed davidbenjamin closed 7 years ago

davidbenjamin commented 7 years ago

A large number of spurious active regions are due to non-reference bases with quals less than 10. The current approach of simply counting non-ref bases is too permissive.

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #3011 via ZenHub