Kiryluk Lab

Genetic Analysis Tools

Here is the list of genetic analysis tools used frequently by our lab:

PLINK: A comprehensive GWAS toolset for data analysis and visualization.
PLINK2: A comprehensive GWAS toolset for data analysis and visualization V2.
Bcftools: Tools for working with VCF and BCF genomic files.
VCFtools: Processes and analyzes VCF files effectively.
REGENIE: A fast analysis toolset for single variant and collapsing tests optimized for large datasets.
SAIGE: Scalable and accurate association tests for GWAS in large datasets.
GCTA: Tools for heritability estimation and meta-analysis.
KING: A toolset for kinship and population structure analysis.
FastPCA: Efficient principal component analysis for population structure inference.
STRUCTURE: Infers population structure and assigns individuals to populations.
ADMIXTURE: Estimates population structure and ancestry proportions.
ANNOVAR: Performs functional annotation of genetic variants.
GATK: A toolkit for variant discovery in high-throughput sequencing data.
TensorQTL: A fast GPU-enabled QTL mapper.