etal/cnvkit

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Tools to process and analyze deep sequencing data.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Official code repository for GATK versions 4 and up

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

MACS -- Model-based Analysis of ChIP-Seq

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. This is a comprehensive update to it.