Mutation Validator

Overview

Mutation Validator is a tool for cross-validating somatic variant calls using orthogonal sequencing data (e.g., targeted deep sequencing). In the TCGA MC3 context, it was used to assess the accuracy of ensemble MAF calls against targeted-sequencing validation data on 3,128 samples (median 126 validation sites/sample).

Used by

• Applied within the TCGA MC3 project to validate somatic calls from the ensemble pipeline against TCGA targeted deep-sequencing data on 3,128 samples; validation was performed on the ISB Cancer Genomics Cloud and Broad FireCloud PMID:29596782

Notes

• Validation sites in MC3 were non-randomly selected by individual TCGA AWGs, biased toward known SMG candidates; false-negative rates for sites missed by all callers cannot be estimated.
• Most validation used the same sequencing chemistry as discovery, limiting its ability to detect systematic errors targeted by filters such as PoN and OxoG.

Sources

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