Code

We have developed the following software to power genomics research and rare disease discovery. All code is open-source and can be found on GitHub.

gnomAD

  • gnomad_methods - python package containing Hail helper functions for gnomAD/MacArthur lab.

  • gnomad_qc - the complete set of scripts used to perform sample and variant QC for the gnomAD v2.1 release.

  • gnomad-browser - code that powers our gnomAD browser.

  • gnomad_lof - code for the gnomAD LoF flagship manuscript.

  • tx_annotation - code associated with the 2020 manuscript entitled "Transcript expression-aware annotation improves rare variant discovery and interpretation.”

  • gnomad-sv-pipeline - code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020).

  • gnomad_lrrk2 - data and code relating to the manuscript "Human loss-of-function variants suggest that partial LRRK2 inhibition is a safe therapeutic strategy for Parkinson’s disease.”

  • gnomad_mnv - code for analyzing multi-nucleotide variants (MNVs) in gnomAD 2.1.

  • gnomad_bigquery - general usage BigQuery library and gnomAD-specific BigQuery import/export.

  • exome-results-browsers - the framework for exploring the results of genetic case-control studies.

  • variant-curation-portal - web application for curating loss of function variants.

  • LOFTEE - plugin for the Ensembl Variant Effect Predictor that improves the detection and filtering of candidate protein-truncating variants.

  • exac_browser - code behind our ExAC browser (now deprecated).

Rare Disease

  • seqr - developed as part of the Broad CMG, this intuitive portal is used by TGG and many of our collaborators to search for causal variants in Mendelian disease families.

  • seqr-loading-pipelines - contains Hail-based pipelines for annotating variant callsets and exporting into the seqr backend data store.

  • tgg-viewer.broadinstitute.org - quickly access sample data and loci in IGV.js. It is specially designed for viewing RNAseq splice junctions and normalized coverage tracks, as well as normalized coverage and copy number calls generated by gCNV.

  • spliceailookup.broadinstitute.org - web application for getting SpliceAI and Pangolin scores.

  • liftover.broadinstitute.org - web application for lifting over genomic intervals or variants.

  • flipbook - tool for quick manual review of local image files.

  • cma-search.broadinstitute.org - web application that makes it easier to search OMIM data based on chromosomal-microarray results.