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.

Mzximum indel size prediction fromHaplotypeCaller

I have a deletion site which is about 1700bp, and I ran my samples with HaplotypeCaller in GATK 3.1 version, and the VCF output file didn't report this deletion. I changed the paramter "activeRegionMaxSize 2000" in the command line.

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