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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 on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
Where do I find population allele frequency files for ContEst?
Hello. I was looking over some of the previous Forum discussion regarding the population allele frequency .vcf files used in the ContEst tool and I am curious if the previous problems with formatting have been resolved. It seems that an error message was coming up that required a reformatting of the file before it would work properly. Also, where are these files downloaded from? Are they included in the GATK Resource Bundle or do you download them from the Cancer Genome Analysis site? In the old CGA site (http://archive.broadinstitute.org/cancer/cga/), they mention that "HapMap population frequencies are available in the download sections" but I do not see any "download sections" on this site. Any help with this would be greatly appreciated.
James E. Jacobs MD, MPH