The current GATK version is 3.6-0
Examples: Monday, today, last week, Mar 26, 3/26/04

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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?


Best Answers


  • myoglumyoglu Posts: 39Member

    Hm, guess Ill be running it all again with really low settings. And then just alter filtering afterwards.

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