How to run the DRAGEN PopGen app on BaseSpace?
The DRAGEN PopGen app on BaseSpace runs the gVCF genotyper; it uses a set of single sample or multisample gVCFs as input and returns a multisample VCF that has an entry for each variant seen in any of the input VCFs/gVCFs. This pipeline does not adjust the genotypes based on population information.
Workflow
Generate single sample/multi-sample VCFs/gVCFs: use an app such as DRAGEN Germline can for this.
Launch the DRAGEN PopGen app using the output from step 1 - the reference used in both steps should match.
DRAGEN PopGen outputs a multisample VCF with one sample column per input sample.
Inputs
Input to the app can be provided in one of these three forms.
Small variant gVCF files: directly select input gVCF files; up to 99 files can be selected.
Datasets containing gVCFs: this can be datasets output by applications, datasets created during uploads etc; up to 100 datasets can be selected.
Project input: select projects that have gVCFs; up to 100 projects can be selected.
For the Datasets and Project inputs, the app, by default, searches for files that end with '.hard-filtered.gvcf.gz'--this behavior can be changed in the Advanced Settings section using the 'Filename Selection Suffix' parameter.
Output
The app outputs a multisample gVCF that has an entry for each variant in any of the input gVCFs.
Limitations
The app currently supports up to around 800 full-size DRAGEN WGS gVCFs. However, the app uses an instance with 5TB disk space; this corresponds to around 800 gVCFs that are ~4GB in size. If the gVCFs are larger in size, then the number of input gVCFs would need to be lowered accordingly in order to use the BaseSpace app.
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