DRAGEN functional equivalence germline SNP and indel discovery in human whole genome sequencing data.
The Whole Genome Germline Single Sample pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and indel discovery in human whole genome sequencing data. When the pipeline runs in the DRAGEN-GATK mode, it produces functionally equivalent outputs to the DRAGEN pipeline.
The workflow requires sample and reference information. The user may decide whether or not to run the pipeline in DRAGEN functional equivalence mode by setting the value of the
The Broad Institute provides various test inputs hosted in GCP that can be used to run the pipeline.
Information and files associated with the sample.
Data associated with the reference genome.
Files used by the DRAGMAP aligner.
Information for variant calling scatter settings.
Information regarding the number of preemptions allowed.
Interval list for the CollectWgsMetrics tool.
The pipeline outputs variant calls, aligned reads, and various metrics files.
Quality control metrics and files output during alignment.
Outputs from aggregating the aligned recalibrated BAM and calculating quality control metrics.
WGS metrics collected using stringent thresholds.
WGS metrics collected using less stringent thresholds.
Files associated with converting the aggregated recalibrated BAM to CRAM.
Reference data hosted in GCP may be found here.