github.com/MethodsDev/ctat-mutations-DV/hg38_ctat-mutations-DV

Automatic Tools and Workflows
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ctat-mutations

RNA-seq variant calling pipeline using DeepVariant with state-of-the-art accuracy.

Version 5.0.0 - Major refactor with DeepVariant integration

Overview

CTAT-Mutations is a comprehensive RNA-seq variant calling pipeline that:

  • Variant Calling: Uses Google DeepVariant v1.9.0 with official RNA-seq model (trained on GTEx data)
  • Alignment: Supports STAR (Illumina short reads) and Minimap2 (PacBio/ONT long reads)
  • Annotation: Integrates dbSNP, gnomAD, COSMIC
This is a companion discussion topic for the original entry at github.com/MethodsDev/ctat-mutations-DV/hg38_ctat-mutations-DV