IKMB DeepVariant Pipeline

This pipeline performs an end-to-end variant calling, starting from raw fastQ files to a single-sample VCF. It has been pre-configured for the CCGA MedCluster.

Documentation

1. What happens in this pipeline?
2. Installation and configuration
3. Running the pipeline
4. Output
5. Troubleshooting

Accuracy

Deepvariant has been shown to be highly accurate to the Genome-in-a-Bottle benchmark sets. The following concordance scores were achieved with this pipeline:

Illumina (NA12878, in-house):

Variant	Recall	Precision
INDEL	0.990528	0.995649
SNP	0.999513	0.999728

Pacbio (NA24385, public):

Variant	Recall	Precision
INDEL	0.982212	0.983814
SNP	0.999244	0.996109

Scoring was limited to the respective genome-in-a-bottle high-confidence regions.