NHGRI supports AnVIL through cooperative agreement awards to the Broad Institute and Johns Hopkins University.

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A somatic copy number variation workflow, representing the Variant Discovery portion of the Somatic CNV Discovery pipeline.

GATK - Best practices for somatic CNV discovery

A fully reproducible example of Processing For Variant Discovery, HaplotypeCallerGVCF, and Joint Discovery workflows.

A basic tutorial for using Hail, a python-based package for working with genomic data.

Compare RNA from tumor samples with corresponding “normal” samples to identify evidence for copy number variations in tumors.

The Optimus pipeline processes 3-prime single-cell transcriptome data from the 10X Genomics v2 (and v3) assay.