Loading homepage
gnomAD methods — Broad Institute Python library for working with gnomAD (Genome Aggregation Database) data using Hail. Provides population genetics analysis including variant filtering with VQSR and r
Use with AI
Install the MCP server or CLI to instantly fetch gnomAD Methods documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/gnomad-methods
Use when working with GWASTools — a Bioconductor R package for quality control, management, and analysis of Genome-Wide Association Studies (GWAS). Covers reading GDS or netCDF genotype data with GdsG
1 shared topic • 3 shared operations
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
1 shared topic • 3 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
1 shared topic • 3 shared operations
Use when working with SNPRelate — a Bioconductor R package for high-performance SNP-based population genetics analysis. Supports principal component analysis (PCA), identity by descent (IBD), Fst esti
1 shared topic • 3 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
1 shared topic • 3 shared operations