# merge_vcfs
Merge VCFs from multiple samples using GATK3.

## Inputs

### Required inputs
<p name="merge_vcfs.merge_vcfs_gatk.in_vcfs_gz">
        <b>merge_vcfs.merge_vcfs_gatk.in_vcfs_gz</b><br />
        <i>Array[File] &mdash; Default: None</i><br />
        VCF files to merged; should be (b)gzipped.
</p>
<p name="merge_vcfs.merge_vcfs_gatk.ref_fasta">
        <b>merge_vcfs.merge_vcfs_gatk.ref_fasta</b><br />
        <i>File &mdash; Default: None</i><br />
        fasta file of reference genome relative to which the input VCF sites were called
</p>

### Other inputs
<details>
<summary> Show/Hide </summary>
<p name="merge_vcfs.merge_vcfs_gatk.docker">
        <b>merge_vcfs.merge_vcfs_gatk.docker</b><br />
        <i>String &mdash; Default: "quay.io/broadinstitute/viral-phylo:2.1.20.2"</i><br />
        ???
</p>
<p name="merge_vcfs.merge_vcfs_gatk.machine_mem_gb">
        <b>merge_vcfs.merge_vcfs_gatk.machine_mem_gb</b><br />
        <i>Int? &mdash; Default: None</i><br />
        ???
</p>
<p name="merge_vcfs.merge_vcfs_gatk.output_prefix">
        <b>merge_vcfs.merge_vcfs_gatk.output_prefix</b><br />
        <i>String &mdash; Default: "merged"</i><br />
        ???
</p>
</details>

## Outputs
<p name="merge_vcfs.merged_vcf_gz">
        <b>merge_vcfs.merged_vcf_gz</b><br />
        <i>File</i><br />
        ???
</p>
<p name="merge_vcfs.merged_vcf_gz_tbi">
        <b>merge_vcfs.merged_vcf_gz_tbi</b><br />
        <i>File</i><br />
        ???
</p>

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> Generated using WDL AID (1.0.0)