HadoopCNV is a MapReduce-based copy number variation caller for genome sequencing data

Simulator for structural variants in various types of next-generation sequencing data

Adaption of the original PennCNV algorithm for whole-genome sequencing data

A tool for somatic structural variant calling using long reads

An example GitHub Action (CI) to build a Singularity container

Easy to run pipeline for CNV calling

Powerful CNV calls filtering pipeline. Focused on fixed loci calling, before visual inspection.

CLI tool to manage the download of large quantities of files from DNAnexus

Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF

DNAnexus platform client libraries

A simple Bash script for making local backups with different views.

A tool to extract LOH blocks from VCF, BAM and FASTA data

Bridge CEA In-House Batch Environment gives a uniform way to access external Batch scheduling systems.

Pareto Task Inference in Python

Docker local slurm cluster

Environment Modules: provides dynamic modification of a user's environment

Lmod: An Environment Module System based on Lua, Reads TCL Modules, Supports a Software Hierarchy

A Slurm cluster using docker-compose

Pedigree creation, plotting, and analytics

Data plotting on gene structures

QuantiSNP

Benchmark of array-based CNV calling tools

An R package to create a pretty Copy Number Variant plot from a segments file

High speed p-value computation for regulatory SNP detection using Motif information

Hierarchical Reasoning Model Official Release

Personal Cancer Genome Reporter (PCGR)