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10-18-2011, 04:48 AM
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#1 |
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Member
Location: Planet Earth Join Date: Jan 2011
Posts: 26
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GATK update changes UnifiedGenotyper output
Hey,
recently I upgraded to the latest version (GenomeAnalysisTK-1.2-1-g33967a4) and I noticed that when I run the UnifiedGenotyper with standard settings, I don't get the "SB" value, that I need for hard-filtering. When I ran the UG of the previous version with standard settings, I got it. How can I set for this parameter in the new version ? Cheers! |
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10-18-2011, 05:23 AM
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#2 |
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Senior Member
Location: UK Join Date: Jan 2010
Posts: 390
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GATK 1.2 release notes: http://www.broadinstitute.org/gsa/wi...TK_release_1.2
From release notes: "SB annotation is no longer calculated by default; use --computeSLOD to turn it on. Users should check out the FS annotation for a Fisher's exact test of strand bias." |
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10-18-2011, 07:41 AM
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#3 |
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Member
Location: Planet Earth Join Date: Jan 2011
Posts: 26
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Thank you for pointing this out!
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