VariantDx
Overview
VariantDx is a custom somatic mutation-calling pipeline developed for matched tumor/normal whole-genome or whole-exome sequencing. It applies paired-sample variant detection with filtering steps to distinguish somatic variants from germline polymorphisms and sequencing artifacts. Designed for use with hg19/GRCh37 reference genome, VariantDx was applied in the Johns Hopkins adenoid cystic carcinoma (ACC) WGS study for high-specificity somatic SNV and indel detection.
Used by
- VariantDx custom somatic-mutation caller used for matched tumor/normal variant detection in 25 ACC WGS samples (hg19 reference); identified 396 somatic mutations in 372 genes (median 14/tumor, range 2–36) and supported discovery of recurrent mutations in Rho-GTPase, axon-guidance, chromatin-regulator, and Notch pathways PMID:26862087
Notes
- Custom pipeline; not widely distributed as a standalone public tool.
- Applied to matched tumor/normal WGS data for somatic SNV and indel calling.
- Results were supplemented by TopHat-Fusion for fusion detection and snpEff for functional annotation in the same study.
- Neoplastic cellularity ≥60% was required for input samples to reduce stromal contamination artifacts.
Sources
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