cn.mops : A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. .
bcbio-nextgen : bcbio-nextgen implements configurable best-practice pipelines for SNP and small indel calling.
inGAP : An integrative next-generation genome analysis pipeline (inGAP), which employed a Bayesian principle to detect single nucleotide polymorphisms (SNPs), small insertion/deletions (indels).
MSG : (Multiplexed shotgun genotyping) A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. .
speedseq : A lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).
ASAP : An open source framework for building and executing a pipeline to preprocess next generation sequence data and variant calls.