Statistical genetics Tools

GCTA (Genome-wide Complex Trait Analysis) is a software package initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been greatly extended for many other analyses of data from genome-wide association studies (GWASs).

Hail is a scalable, cloud-native genomic analysis tool designed for large datasets. It provides a query language for genomic data and supports batch computing for efficient variant calling and other analyses.

IMPUTE2 is a genotype imputation and haplotype phasing tool that uses a multi-population reference panel to impute missing genotypes in genome-wide association studies (GWAS), enabling researchers to increase the density of genetic markers and improve statistical power for association analyses.

LDhat is a package written in the C and C++ languages for the analysis of recombination rates from population genetic data.

LDsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.

MuSiC utilizes cell-type specific gene expression from single-cell RNA sequencing (RNA-seq) data to characterize cell type compositions from bulk RNA-seq data in complex tissues. By appropriate weighting of genes showing cross-subject and cross-cell consistency, MuSiC enables the transfer of cell type-specific gene expression information from one dataset to another.