Version history

[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 v0.11.9 for read-level QC and summary.
  • STAR v2.7.9a for read alignment to reference genome.
  • Samtools v1.15.1 for alignment sorting, indexing, and statistics.
  • GATK v4.2.6.1 for alignment post-processing, variant calling, and filtration.
  • Tabix v1.11 for indexing VCF files.
  • SnpEff v5.0 for variant annotation.
  • Ensembl VEP v104.3 for variant annotation.
  • MultiQC v1.12 for 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.

Thanks to everyone that contributed to this release. Special thanks to @maxulysse, @FriederikeHanssen, and @chris-cheshire for your reviews and valuable suggestions.