RADIA
Overview
RADIA (RNA and DNA Integrated Analysis) is a somatic variant-calling tool designed to leverage both DNA (exome or genome) and RNA-seq data simultaneously. By integrating matched tumor/normal DNA and tumor RNA evidence, RADIA can improve specificity and sensitivity for somatic SNV detection, particularly for variants with RNA-level support that may be filtered as artifacts in DNA-only callers. It was developed at UCSC and was part of the TCGA multi-caller consensus mutation-calling pipeline.
Used by
- One of four mutation callers (MuTect, Indelocator, VarScan, RADIA) used in ≥2-caller consensus strategy for somatic mutation detection across 820 TCGA diffuse glioma exomes; combined calls contributed to identification of 75 significantly mutated genes including 45 novel glioma associations PMID:26824661
- One of seven somatic callers in the TCGA MC3 ensemble pipeline, run on DNAnexus cloud across ~10,510 TCGA tumor/normal pairs PMID:29596782
Notes
- Requires matched tumor/normal DNA and optionally tumor RNA-seq as input.
- Uses RNA evidence as a supporting filter rather than calling variants on RNA alone.
- Developed as part of the TCGA somatic mutation calling framework; frequently used in TCGA pan-cancer analyses with a ≥2-caller consensus filter.
- Consensus filtering (requiring variant support from ≥2 callers) reduces false-positive rate at the cost of some sensitivity for low-VAF variants.
Sources
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