GATK Analysis Parameters

Hi! I am new to next gen sequencing and started working with Ion Torrent's PGM for the Targeted Gene Sequencing using the AmpliSeq Custom Panel. I need to get the analysis going and asking for help from others. I have been reading a lot and have a better understanding of the workflow but not having bioinformatics background has been difficult to run the GATK in our Linux system. Can anyone help me with analysis parameters? Or anywhere I can find them? I have 175 patients and 31 genes in my panel.


Best Answers


  • nikmalnikmal Member

    This document is very helpful:

    For variant calling, this is also very helpful:

    Though I'm not sure if you need to tweak some parameter(s) especially for Ion Torrent data.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Which step are you having trouble finding parameters for?

  • vramachavramacha Member

    I am not doing the analysis but have to help and direct the Bioinformatician who has been using GATK for the microbial data analysis generated by Ion Torrent's PGM. He has no experience in using human NGS data in GATK. We didn't know where to start and decided on a test run using the Ion Torrent data generated for a set of positive controls (where we know what the expected mutations are). To start the analysis, we wanted to have the parameters.


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    I see. The problem is that it depends what analysis you want to do. The GATK is not a single tool, it is a toolbox that you can use for many different analyses. If you tell me what you want to do, I can point you to the right tools and parameters.

  • vramachavramacha Member

    Thanks for your help! Our aim is to identify rare genetic variants in the unrelated patient cohort (N=175 ; drug induced arrhythmias). We used Ion Torrent's PGM and AmpliSeq Technology for our Custom Panel - with 31 genes, target size 750kb, minimum coverage 30X.

    Looking at the Best Practices Workflow - Calling Variants with the GATK - we will be performing all the 3 phases of the workflow. But don't know what tools to use.

    Our Microbial Bioinformatician has used the following process previously:

    Hope I have given you all the info. If not please let me know. I will send anything you want.

    Thanks again

  • vramachavramacha Member

    Thanks Geraldine and am coming back to you for sure!

  • vramachavramacha Member
    edited May 2013

    HI Geraldine!

    We had data on patients for whom we know the mutation status and are using them as control data for the practice/preliminary GATK runs. After obtaining guidance from you, our Bioinformatician Adam is using this pipeline.

    • tmap - for Ion Torrent Data he said this is best
    • SortSam
    • MarkDuplicates
    • AddOrReplaceReadGroups
    • RealignerTargetCreator
    • IndelRealigner
    • BaseRecalibrator
    • BaseRecalibrator
    • PrintReads
    • ReduceReads
    • UnifiedGenotyper
    • VariantFiltration

    Would like to know your thoughts/suggestions.


    Post edited by Geraldine_VdAuwera on
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