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Clarification of --normal-artifact-lod in FilterMutectCalls
The FilterMutectCalls tool doc says:
If the normal artifact log odds is larger than the threshold, then FilterMutectCalls applies the artifact-in-normal filter. For matched normal analyses with tumor contamination in the normal, consider increasing the normal-artifact-lod threshold.
This is what I understand:
The normal atrifact log odds is the threshold above which an artifactual site detected in the normal will be used to filter any variants at that site (assuming this is just a shared artifact). If there is tumor contamination of the normal, an apparent artifact in the normal may just represent tumor contamination. Hence, this threshold should be raised if we suspect tumor contamination of the normal.
Am I right?