DepthOfCoverage and DiagnoseTargets: our plans for development and support

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,365Administrator, GATK Developer admin

We have decided to continue providing and supporting DepthOfCoverage and DiagnoseTargets for the foreseeable future. Going forward, we'll try to integrate them and develop their features to address the main needs of the community. To this end we welcome your continuing feedback, so please feel free to contribute comments and ideas in this thread.

To all who took the time to tell us what you find useful about DoC and DT (and what you wish it could do), a big thank you! This is always very useful to us because it helps us identify which features are most valuable to our users.

Geraldine Van der Auwera, PhD

Comments

  • mengyuankanmengyuankan Posts: 2Member

    Thanks Geraldine. A newbie question: what's the difference between DepthOfCoverage and DiagnoseTargets, and which one do you recommend to use (or both)?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,365Administrator, GATK Developer admin

    The two are somewhat convergent, but basically DepthOfCoverage allows you to evaluate the depth of coverage in your data at certain sites or over intervals generally, whereas DiagnoseTargets is more specifically designed to evaluate the quality of data covering exome target intervals. The best thing to do is to read their respective documentations pages (links below) and see which sounds like it will suit you needs best.

    http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html

    http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_diagnostics_targets_DiagnoseTargets.html

    Geraldine Van der Auwera, PhD

  • kevyinkevyin Posts: 11Member
    edited June 2013

    Hi @Geraldine_VdAuwera and thanks for support on this.

    The DepthOfCoverage documentation mentions -nt as a parallelism option but I get an error.

    ##### ERROR MESSAGE: Invalid command line: Argument nt has a bad value: The analysis DepthOfCoverage aggregates results by interval. Due to a current limitation of the GATK, analyses of this type do not currently support parallel execution. Please run your analysis without the -nt option.

    My command line:
    java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -I ExampleBAM.bam -R exampleFASTA.fasta -o ./test_coverage_out -nt 4

    Is this an error in the documentation? Or am I missing something?

    Thanks.

    Post edited by kevyin on
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,365Administrator, GATK Developer admin

    Hi @kevyin,

    DOC is currently set up to aggregate statistics over intervals by default, which is incompatible with the -nt mode. You can disable this behavior by using the --omitIntervalStatistics flag, which should make -nt work. Let me know if you have any issues with that.

    We may change the default behavior in future; in any case we will add a note about this to the documentation. Thanks for reporting this!

    Geraldine Van der Auwera, PhD

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