Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

QC of genotypes

How I can remove SNPs with Low quality or out of Hardy-Weinberg in my VCF file. In column 7 of my VCF file I have only "LowQual" or ".".
There is no "PASS" word in this column. Is there something wrong in my VCF or any problem with UnifiedGenotyper procedure? thanks

Best Answer


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