Bug Bulletin: The GenomeLocPArser error in SplitNCigarReads has been fixed; if you encounter it, use the latest nightly build.

Haplotypecaller, change setting after the run!

myoglumyoglu Posts: 39Member

--stand_emit_conf and --stand_call_conf is by default set to 30

Everything lower will be "LOWQUAL", but is it possible to set --stand_emit_conf and --stand_call_conf set to 2, without running everything one more time?

Thanks!

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