bigsnpr

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 • 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

3 shared topics • 2 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

SHAPEIT4/5 — statistical haplotype phasing for SNP array and whole-genome sequencing data. SHAPEIT5 is the current production version, providing phasing of common variants (MAF >= 0.1%) via phase_comm

3 shared topics • 1 shared operation

Stacks is a software pipeline for building loci from short-read sequencing data (RAD-seq, GBS, ddRAD, 2b-RAD) for population genomics and phylogeography. Supports de novo and reference-guided assembly

3 shared topics • 1 shared operation