
Brian Haas
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Mutect2 Tumor-only calling of variants with high AF?
When running Mutect2 in tumor-only mode, it seems that most any variants with a high allele fraction (>0.4 or so) tend to be classified as 'germline' variants by the filtering step. In matched tum...
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Mutect2 PoN allele-specific or less specific position-based?
Can you please confirm that the panel of normals is excluding variants based on chromosome position and not requiring allele-specific matching? ie. a G->A variant in the tumor sample may be filtere...
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Current Mutect2 somatic variant PoN logic
Can I please confirm that this is the logic being used in the current PoN creation step: ==== Any candidate PoN site must occur in at least 2 samples (as per the default for --min-sample-count). If...