Tagged with #badmatefilter
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Created 2012-07-23 23:54:58 | Updated 2012-07-23 23:54:58 | Tags: badmatefilter gatkdocs
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A new tool has been released!

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