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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
Use with AI
Install the MCP server or CLI to instantly fetch VCFtools documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/vcftools
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
3 shared topics • 3 shared operations
Use when working with bigsnpr — an R package for analysis of massive
3 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
3 shared topics • 2 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
2 shared topics • 3 shared operations
CNVpytor — Python tool for copy number variation (CNV) detection from whole-genome sequencing (WGS) BAM/CRAM files. Analyzes read depth signals with adjustable bin sizes, calls deletions and duplicati
3 shared topics • 1 shared operation