INDEL hard filter

2nelly2nelly SwitzerlandMember

Hi GATK team,

I was wondering why according to the guidelines included in this link http://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set , you don t suggest the usage of a MQ threshold for indel filtering.

Thank you in advance!

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