Hail is an open-source, scalable framework for exploring and analyzing genetic data. Starting from sequencing or microarray data in VCF and other formats, Hail can, for example:

generate variant annotations like call rate, Hardy-Weinberg equilibrium p-value, and population-specific allele count
generate sample annotations like mean depth, imputed sex, and TiTv ratio
load variant and sample annotations from text tables, JSON, VCF, VEP, and locus interval files
generate new annotations from existing annotations and the genotypes, and use these to filter samples, variants, and genotypes
find Mendelian violations in trios, analyze genetic similarity between samples via the GRM and IBD matrix, and compute sample scores and variant loadings using PCA
perform association analyses using linear, logistic, and linear mixed regression, and estimate heritability