We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
What is the size of the internal window used by gatk haplotypecaller's sliding window approach?
Hello gatk community,
Since gatk haplotypecaller is ran by a sliding window approach, the variant calling on each position seems to also depend on the presence/type/absence of variants on the flanking region. I guess such effects will stem from the size used by the sliding window. For example, a longer flanking region that contains more variants will tend to help a new read to be better aligned on the current position as I suppose. Could you please let me know what is the internal sliding window size used by gatk HC?