gatk4 RNA variant calling pipeline
[1.0.0] - 2022-06-20
First production release of the pipeline with the latest software versions.
This version is based on GATK4 best-practices for RNAseq [Ref] and it includes:
FastQC v0.11.9for read-level QC and summary.
STAR v2.7.9afor read alignment to reference genome.
Samtools v1.15.1for alignment sorting, indexing, and statistics.
GATK v220.127.116.11for alignment post-processing, variant calling, and filtration.
Tabix v1.11for indexing VCF files.
SnpEff v5.0for variant annotation.
Ensembl VEP v104.3for variant annotation.
MultiQC v1.12for QC summary report.
- Scatter method i.e., split one gene interval list into many interval files to run multiple processes in parallel to speed up analysis.