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gatk4 Allelic CNV

anand_mtanand_mt Member
edited August 2017 in Ask the GATK team

Hi,

I have been using gatk4 alpha for copy number analysis. I have created PoN and did segmentation. Now I want to check for allelic CN which requires heterozygous sites. For now I am using germline heterozygous variants. is it okay ? Are there any suggestion on selecting variants ?

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