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.
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.
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!

Recommended Pipeline

mike_boursnellmike_boursnell Member
edited July 2012 in Ask the GATK team

Hi. Could you suggest a recommended pipeline for us. We receive BAM files from our sequencing - the sequencing is mostly targetted regions (~10MB) and the species is dog, so we don't want to skip known SNPs as different breeds have different known SNPs. We have one BAM file for each dog sample, usually about 10 samples.

I have looked at the guidelines (Best Practice Variant Detection) for this but I'm a bit confused...


  • SophiaSophia Member

    After that, to obtain all samples in one vcf file, you might run the UnifiedGenotyper analysis listing all processed bam files in the same command.

  • SophiaSophia Member
    edited July 2012

    PS.: GATK does not know about dog SNPs and will not consider or skip them unless you tell it to (e.g. by inputing a vcf or similar positions file in some of the commands). That means you will get unfiltered results to start with.

  • Thanks for those comments.

    In the Best Practice Variant Detection it has these options:

    • Fast: lane-level realignment at known sites only and lane-level recalibration
    • Fast + sample-level realignment
    • Better: sample-level realignment with known indels and recalibration
    • Best: multi-sample realignment with known sites and recalibration

    Are you suggesting using the last of these options? (Best...)

    Can this be done through the DataProcessingPipeline Queue script?

  • SophiaSophia Member

    Mike, do you have lists of known SNPs from dog? Which dog reference genome version are you using?

  • Hi Sophia. We have a list of known SNPs from canFam3. Do you have a list as well? If so I wouldn't mind comparing it to ours. We don't have a list of known Indels for the IndelRealigner though.

Sign In or Register to comment.