# 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**

1. Generate single sample/multi-sample VCFs/gVCFs: use an app such as DRAGEN Germline can for this.
2. Launch the DRAGEN PopGen app using the output from step 1 - the **reference** used in **both steps** should **match**.
3. 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.

1. Small variant gVCF files: directly select input gVCF files; up to **99 files** can be selected.
2. Datasets containing gVCFs: this can be datasets output by applications, datasets created during uploads etc; up to **100 datasets** can be selected.
3. 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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