GATK4 -Create Somatic Panel of Normals

Description

Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2.

Parameters

• Minumum sample count (Integer) [2]

Details

Create a panel of normals (PoN) containing germline and artifactual sites for use with Mutect2. The tool takes multiple normal sample callsets produced by Mutect2's tumor-only mode and collates sites present in two or more samples into a sites-only VCF. The PoN captures common artifactual and germline variant sites. Mutect2 then uses the PoN to filter variants at the site-level.

Based on GATK4 CreateSomaticPanelOfNormals tool. For more detailed information, see GATK documentation,

Output

• VCF file with the PoN

References

This tool is based on the GATK4 package.

For instructions on citing GATK4, please see GATK FAQ