Official code repository for GATK versions 4 and up

status-active lang-java lang-python domain-bioinformatics interface-cli task-workflow task-file-io status-published method-machine-learning method-statistics role-toolkit scope-swissknife entity-nucleic-acid entity-sequence domain-genomics task-variant-analysis

• Updated Jul 30, 2026
• Java

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

status-active lang-python lang-cpp domain-bioinformatics interface-cli method-deep-learning role-application status-published scope-focused entity-nucleic-acid entity-sequence interface-gpu domain-genomics task-variant-analysis

• Updated Mar 19, 2026
• Python

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

status-active lang-python lang-perl domain-bioinformatics interface-cli role-application status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid entity-sequence method-rule-based domain-genomics task-variant-analysis

• Updated Jul 24, 2026
• Perl