Heads up:
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.
Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
Attention:
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!

Testing Intel Arria® 10 GX FPGA implementation of HaplotypeCaller (PairHMM)

Hi,
I am a researcher from Chinese of Academy of Sciences.
I am trying to test the FPGA implementation of the HaplotypeCaller (PairHMM) on GATK 3.8-0-ge9d806836, using a Intel Arria® 10 GX FPGA (Arria 10, 10AX115N2F40E2LG).
I found a very useful link in gatk forum (https://gatkforums.broadinstitute.org/gatk/discussion/10501/testing-fpga-implementation-of-haplotypecaller-pairhmm), which says "Currently supported cards are the Nallatech 385a and Inspur F10A cards". And I tired the Intel® FPGA PairHMM Accelerator for Genomics Kernel Library on the website of Intel (https://downloadcenter.intel.com/download/27342/Intel-FPGA-PairHMM-Accelerator-for-Genomics-Kernel-Library-GKL-).
However, from my tests it doesn't work for Intel Arria® 10 GX FPGA. Is there any plan to support Intel‘s own board of FPGA implementation?
Kind regards,
Gong

Answers

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