Tagged with #badmatefilter
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Created 2013-02-21 11:11:56 | Updated | Tags: badmatefilter

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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.

Any idea??

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

Created 2012-10-11 21:54:39 | Updated 2012-10-18 01:33:56 | Tags: unifiedgenotyper badmatefilter mappingqualityfilter

Comments (13)

It was a bit unclear what the BadMateFilter is doing in the documentation. Any information would be appreciated!