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AfshinLab / BLR

MIT License
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gatk HaplotypeCaller filters out QUAL < 30 by default #67

Open pontushojer opened 12 months ago

pontushojer commented 12 months ago

Current config defaults has a filter for lowQual that is QUAL < 15 but this currently does not do anything as no variants outputted with QUAL < 30 from gatk. This can be changed by using the flag -stand-call-conf 15.

Issue copied from FrickTobias

https://github.com/FrickTobias/BLR/issues/248