snpStats

Use when working with bigsnpr — an R package for analysis of massive

2 shared topics • 2 shared operations

EIGENSOFT smartpca -- C/C++ tool for principal component analysis of genome-wide SNP genotype data. Computes eigenvectors and eigenvalues for population structure analysis, ancestry inference, stratif

2 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 • 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

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