Combine two panel-of-normals files
AnsweredHi, 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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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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