Software versions

The TSOPPI v0.3 container is based on continuumio/miniconda3 docker image version 4.10.3p1. PCGR/CPSR v1.0.0 is installed on top in the recommended setup, contributing two Conda environments with the following programs directly called by TSOPPI:

• pcgr environment:

  • PCGR and CPSR v1.0.0: small variant annotation (somatic variant evaluation and assessment of potential cancer predisposition changes);

  • Python v3.7.12: execution of internal TSOPPI Python scripts;

  • samtools v1.10 (using htslib v1.10.2): extraction of small variants’ genomic contexts for the purposes of mutational signature plotting (tool faidx);

  • bedtools v2.30.0: DNA sample coverage- and whitelist-related analyses (tool intersectBed).

• pcgrr environment:

  • R/Rscript version v4.1.2: execution of internal TSOPPI R-scripts - all of plotting;

  • Python v3.10.2: execution of internal TSOPPI Python scripts.

An additional Conda environment (bcftools_env) is present in the TSOPPI image in order to provide access to:

• bcftools v1.9 (using htslib v1.9): assessment of small variant support within RNA samples (tools mpileup and norm).

Static Java (jdk-11.0.6) and Picard tools (v2.26.2) packages are utilized for the (optional) assessment of sequencing artifact metrics (tools AddOrReplaceReadGroups and CollectSequencingArtifactMetrics).

(last updated: 2022-03-03)