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"UKNOWN" zygosity in CSV file

Hi There,
I am using GATK 3 . Recently i checked two CSV and bam file for couple, that both of them are carrier of one pathogenic variant, But in CSV file, the zygosity of this variant in both of them labeled as "Unknown" and not Heterozygote.
I have two question:
1- What is main criteria to determine "zygosity" of one variant in GATK?
2-How can i eliminate false negative (or false positive) variants in final VCF (by GATK)?

Than you


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Mojtaba,

    Can you tell us how you generated the CSV file?

    1) If you use HaplotypeCaller to generate the variants, you can read more about the algorithm in the Methods and Algorithms section.

    2) You can use VQSR or the new CNN workflow.


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