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 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.

Quality recalibration with the latest GATK jar (GenomeAnalysisTK-2.1-9-gb90951c)

LavanyaLavanya Member
edited September 2012 in Ask the GATK team

Hi,

I have been using GATK for realignment and recalibration steps on mapped BAM file before we call SNP calling. I just downloaded the latest GATK jar (GenomeAnalysisTK-2.1-9-gb90951c) and started testing these walkers.

With the earlier version of GATK, I was calling CountCovariates followed by TableRecalibration as a part of Quality score recalibration.

Essentially CountCovariates and TableRecalibration options are not available in the latest GATK jar. I would like to know the equivalent steps.

I suspect with the latest GATK version, both these steps has been merged as BaseRecalibrator?? But the output from BaseRecalibrator is recal_data.grp. Can anyone explain about Quality score recalibration step in the latest GATK version. Thanks.

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    Yes, you've got that right. For your info, the .grp file is called a GATKReport file. You can find out more about this type of file here.

    Regarding multithreading, this article details how it works and what are the limitations (e.g. which types of walkers don't support it). However, here's a hint for simplicity's sake: to test whether a tool supports multithreading, try to run a simple command with the tool using the -nt option. The program will quickly exit out with an error if the tool doesn't support multithreading; whereas if it does, it will start running normally.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,
    That's correct -- since version 2.0, base recalibration is now done with the base recalibrator tool. Please see the documentation for details of how to use it.

  • LavanyaLavanya Member

    Thanks Geraldine for your response. I will try to run the command line to see whether all reports are being generated.
    I have read the documentation and I still have the following doubts...
    1. The output from base recalibrator is .grp file. Is it similar to csv file?
    2. With old GATK versions, we used to do count covariates and table recalibration and we got a bam as the finally output. We used this bam to call SNP. But with the latest GATK, I am bit confused about generating bam file after .grp file is generated? Am I missing something here.. which I am sure.. :(
    3. Can I use the multi threaded mode for baserecalibrator?

    Thanks again.
    Regards

  • LavanyaLavanya Member

    Oh ok. I just read the link under http://www.broadinstitute.org/gatk/guide/topic?name=methods-and-workflows. So should I use -T PrintReads module to generate bam using .grp as input...
    Also please let me know whether multi theaded is available for both baseRecalibrator and PrintReads module...

    Please correct me if I am wrong..

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    Yes, you've got that right. For your info, the .grp file is called a GATKReport file. You can find out more about this type of file here.

    Regarding multithreading, this article details how it works and what are the limitations (e.g. which types of walkers don't support it). However, here's a hint for simplicity's sake: to test whether a tool supports multithreading, try to run a simple command with the tool using the -nt option. The program will quickly exit out with an error if the tool doesn't support multithreading; whereas if it does, it will start running normally.

  • LavanyaLavanya Member

    Great thanks Geraldine....

Sign In or Register to comment.