MPRAnator

GREML (GCTA) — genome-based restricted maximum likelihood analysis for SNP heritability estimation, genetic correlation, mixed linear model association (MLMA), and COJO conditional analysis. Use when

2 shared topics • 1 shared operation

Gubbins — rapid phylogenetic analysis of recombinant bacterial whole genome sequences. Iteratively detects recombination hotspots with elevated SNP density while constructing clonal frame phylogenies.

2 shared topics • 1 shared operation

GWAS Catalog tools (gwas-sumstats-tools) are EMBL-EBI utilities for reading, writing, validating, and formatting genome-wide association study (GWAS) summary statistics in the GWAS-SSF standard format

2 shared topics • 1 shared operation

RTG Tools — Java-based toolkit from Real Time Genomics for haplotype-aware variant call comparison, VCF filtering, statistics, and pedigree analysis. Primary use: vcfeval for benchmarking variant call

2 shared topics • 1 shared operation

snpStats is an R/Bioconductor package for GWAS (genome-wide association study) and population genetics analysis. It provides SnpMatrix and XSnpMatrix objects for efficient SNP data storage, PLINK bina

2 shared topics • 1 shared operation