RTG Tools

Use when working with MungeSumstats — a Bioconductor R package for standardizing and quality-controlling GWAS (genome-wide association study) summary statistics. Covers the full MungeSumstats pipeline

2 shared topics • 2 shared operations

PLINK/SEQ — open-source C/C++ library and command-line tool (pseq) for working with human genetic variation data from large-scale resequencing projects. Use when working with VCF loading, variant filt

2 shared topics • 2 shared operations

TRAPD — Toolkit for Rare variant Association from Population Data. Tests gene-level rare-variant burden in case-control studies using population databases (gnomAD, TOPMed) as controls. Implements adap

2 shared topics • 2 shared operations

VCFtools — C++ toolkit for filtering, comparing, summarizing, converting, and manipulating VCF (Variant Call Format) and BCF files. Provides site and individual-level filtering, allele frequency calcu

2 shared topics • 2 shared operations

Poetry is the Python dependency management and packaging tool for creating reproducible projects with pyproject.toml and poetry.lock. Use this skill for dependency resolution, virtual environment isol

2 shared topics • 1 shared operation