Today, the commercialization partnership between the Broad Institute and Appistry officially ended. As we announced on April 2, the Broad Institute has opted to retain commercial distribution rights to its NGS analysis software. This means that as of today, April 15, 2015, anyone seeking licenses to the GATK or the tools underlying the Cancer Genome Analysis (CGA) Suite (specifically MuTect and ContEst) must contact the Broad Institute for information at

You will notice some changes on our website now that Appistry is no longer distributing Broad Institute tools. If you have come to this page from a prior active link, please consult the FAQ below to find the information you need. And feel free to leave any other questions you may in the comments. We want to make sure this transition is the least disruptive as possible to your continued ability to use leading tools for genomic analysis in your pipelines.

I’m a current licensed user of the GATK or the Cancer Genome Analysis (CGA) Suite. Where do I go if I have questions about support?

Appistry will continue to support all licensed users of the GATK or the CGA Suite until their licenses expire. Please contact with questions or access the Appistry Support Portal to get help.

I’m a current licensed user of the GATK or the CGA Suite, but I have questions about what happens when my license expires. Who do I contact?

As of today, all inquiries regarding licenses to NGS analysis tools from the Broad Institute must be directed to the Broad. You can reach them at

I’ve never had a license from Appistry, but I’m interested in licensing the GATK or MuTect and other tools from the Broad Institute. Who do I contact?

Contact the Broad at

Is Appistry still selling NGS analysis software?

Yes, and we have expanded our offerings through GenomePilot, an intuitive application for running NGS analyses. GenomePilot offers access to a collection of tools and preconfigured pipelines for NGS analysis. You can use Broad Institute software within GenomePilot, as well as other commercial, open-source, or proprietary tools. Best of all, you don’t need any sophisticated command-line or scripting experience to configure the tools into complex processes. If you haven’t yet heard about GenomePilot, check out the demos on our website, or watch our latest webinar, which features an in-depth demonstration of the software.

Wait. I thought Appistry was no longer distributing the GATK or MuTect. But some GenomePilot processes use these tools. Does that mean I get the tools with GenomePilot?

No. Appistry has developed several preconfigured processes that use Broad Institute tools, such as BQSR, the Haplotype Caller, and MuTect. But to use these processes within GenomePilot, you will need to have or acquire a separate license to the appropriate tools from the Broad Institute. This is no different from how GenomePilot will work with other commercial tools. GenomePilot also includes a number of non-GATK variant discovery tools, including SomaticSniper and SAMtools mpileup for calling SNPs and indels, Pindel for calling structural variants, and ControlFREEC for copy number variation—and we plan to add more. Let us know what tools you’d like to use in GenomePilot!

Is there someone at Appistry I can speak to about this transition?

Yes. You may leave a comment on this blog or email Maggie Piasecki, who will see that you are put in touch with the right person to help you.

Trevor Heritage

Trevor Heritage

Trevor Heritage leads Appistry’s marketing and business development organizations. His diverse background in pharmaceuticals, chemicals, and computer science makes him a seasoned commentator on the challenges associated with running modern labs and capitalizing on new technologies.