Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?