Combine two panel-of-normals files

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Robin Mjelle

• July 08, 2022 12:03

Hi, I have made a PON from my normal samples and want to combine this with the PON from GATK. Is this possible? Or any other way of using both when running mutect2?

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  Philipp Hähnel

  • July 08, 2022 15:24

  Hi Robin,

  you can use MergeVcfs for merging the two PoN vcfs:

  gatk MergeVcfs -I pon1.vcf.gz -I pon2.vcf.gz -O merged_pon.vcf.gz

  Best,

  Philipp

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  Steffen Møller Bøttger

  • October 02, 2023 11:14
  • Edited

  This does seem to work. But according to MergeVcfs:

  If there are samples, those must be the same across all input files.

  I have successfully run it with one VCF with samples and one without, so the requirement is not strict, it seems.

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