DepthOfCoverage and DiagnoseTargets: our plans for development and support

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,162Administrator, GATK Dev 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: 8,162Administrator, GATK Dev 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: 8,162Administrator, GATK Dev 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

  • SerenaRhieSerenaRhie Posts: 7Member

    Hello, I want the concise depth of coverage summary as well as the per-location covering number of bases for my RNA-Seq data.
    With not splitting the N containing reads, what does DoC exactly do with -U ALLOW_N_CIGAR_READS option? Is it still counting the bases in the CIGAR array represented as matched? I think the bases represented as N in CIGAR should not be counted, just as the deletions (D) are treated. (Maybe an option such as --includeNBases might be appropriate for special cases.)
    A good explanation will be helpful to decide the DoC or not.

    And please do something with the last line of the ERROR MESSAGE "Notice however that if you were to choose the latter, an unspecified subset of the analytical outputs of an unspecified subset of the tools will become unpredictable.", which I think is totally nonsense! :smile:

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,162Administrator, GATK Dev admin

    @SerenaRhie,

    Hah, I think the developer who wrote that error message was feeling particularly sarcastic that day. I'll see what we can do to make that a little more informative.

    Regarding the behavior question, I believe the Ns in the CIGAR are correctly interpreted as not contributing any coverage.

    That said, you could run DoC after running the SplitNTrim step, which will give you effective depth after processing.

    Geraldine Van der Auwera, PhD

  • SerenaRhieSerenaRhie Posts: 7Member
  • MUHAMMADSOHAILRAZAMUHAMMADSOHAILRAZA Beijing Institute of Genomics, CASPosts: 45Member

    Hi @Geraldine_VdAuwera

    i try to use -nt option while running DoC tool. I added -omitIntervalStatistics. But it still prompts an error.

    My command was:
    java -Xmx15g -jar /softwares/GTK/GenomeAnalysisTK.jar -T DepthOfCoverage \
    -log DepthofCov/depth.log -nt 15 -omitIntervalStatistics \
    -R /Ref/human_g1k_v37.fasta \
    -I /DepthofCov/CHG000691_2_3bam.list \
    -geneList /Ref/humanRefseqROD_Final.refseq \
    -o /DepthofCov/HM_trios_Samples

    Error Message:

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
    ERROR
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR
    ERROR MESSAGE: Argument with name 'omitIntervalStatistics' isn't defined.
    ERROR ------------------------------------------------------------------------------------------

    Can you help me how to resolve this issue?
    Thanks..

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,162Administrator, GATK Dev admin

    Try using two dashes instead of one (--).

    Geraldine Van der Auwera, PhD

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