We believe in making our code open source. The following GitHub repositories contain genomics tools you may find useful:
- seqr is a software tool we use for searching for causal variants in Mendelian disease families.
- LOFTEE is a plugin for the Ensembl Variant Effect Predictor that improves the detection and filtering of candidate protein-truncating variants.
- exac_browser is the code behind our ExAC browser.
- clinvar provides tools to parse NCBI’s ClinVar database, and a flat file representation thereof.
- gene_lists is a collection of gene lists for genome-wide analyses.
- minimal_representation is a collection of scripts for canonicalizing the representation of genomic variants.
- denovolyzeR is an R package for testing the gene-wise burden of de novo variants in disease families compared to random mutational expectations.
- igv_plotter automates the generation of IGV screenshots for sequencing reads at variant sites of interest.