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