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.

CombineGVCFs does not work on haploid genotypes

It converts a haploid genotype 0 or 1 to a dot; for example:
GT:DP:GQ:MIN_DP:PL 0:53:99:18:0,666 to .:53:99:18:0,666


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