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Rescuing variants Tumor In Normal Contamination--AF fit
I was looking at GATK talks/ppt, "Filtering somatic variants--rescuing TiN variants and removing artifacts" (https://www.broadinstitute.org/gatk/events/slides/1506/GATKwr8-S-4-Filtering.pdf) and I was wondering how to rescue the variants that have tumor contamination in the normal sample. I can see the presentation uses allelic fractions to make a best fit line, but how is the mutation TiN fit line being calculated??? How do I know which variants can be rescued? Or is this something MuTect already has built-in functionality for?