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[GATK 4 beta] FilterByOrientationBias for matched normals

mattimatti FinlandMember

In the manual / help-page of CollectSequencingArtifactMetrics, it is said that CollectSequencingArtifactMetrics tool should be run for both the normal sample and the tumor sample, if the matched normal is available. Could you elaborate a bit how to do this, since it appears that the --preAdapterDetailFile parameter in CollectSequencingArtifactMetrics and the --input parameter in CollectSequencingArtifactMetrics cannot be defined more than once. Should I, for example, apply the CollectSequencingArtifactMetrics tool twice for the VCF files and if, yes, does the order of T and N matter.

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