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.

Haplotype caller speed

Hi ,
I am using haplotype caller for SNP identification, after running 1 week, I only finished 40% of the data (nct=20). How can I speedup the process? I can't run jobs>1 week. And using nct=20 is probably all I can. Is the newer version improved the speed?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    We have addressed questions about HaplotypeCaller's performance speed many times on this forum. Please search past articles and you will find some helpful discussions. If you still have questions after reading them, feel free to post follow-up questions as comments in those threads.

  • yg1yg1 Member

    I have used reduced bam and managed to finish the analysis.

Sign In or Register to comment.