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Default filters for UnifiedGenotyper

Hi,

My question is: Is it possible to disable any of the default read filters in UnifiedGenotyper tool?

Concretely, i've been experiencing some problems with BadMateFilter. I work in a non-model species which has a relatively high fragmented assembly. Due to fragmentation I usuallly find reads with mate mapped to a different contig, which provokes a non negligible loss of callable sites.

Any idea??

Congratulations for you nice suite of tools and thanks in advance
Jose

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,641Administrator, GATK Developer admin

    Unfortunately that's not possible; the filters are needed to prevent the UG from blowing up on problematic reads. Perhaps you can try getting rid of the mate information altogether?

    Geraldine Van der Auwera, PhD

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