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Call DeNovo variants from vcf files created with the CNN pipeline - vcf join step

manolismanolis Member ✭✭✭
edited March 2019 in Ask the GATK team

Hi,

I want to use the vcf files created with the CNN pipeline for De Novo calling (calling using the GATK steps). In the case of the VQSR pipeline the vcf join step was done upstream (g.vcf , GenomicsDBImport) and at the end just I needed to extract the trios data in a new vcf, data already joined correctly.

What is the best tool to use for join 3 CNN-vcf files (trios family) or steps to do?

I saw that in some cases the same variant present in two or more vcf, in some vcf was called as "PASS" (ex: proband + mother) and in the other as "no-PASS" (ex: father)...

Many thanks

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