[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 v22.214.171.124for 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.
Thanks to everyone that contributed to this release. Special thanks to @maxulysse, @FriederikeHanssen, and @chris-cheshire for your reviews and valuable suggestions.