Combine two panel-of-normals filesAnswered
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?
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
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