depth of coverage link

estif74estif74 Saint Paul, MN, USAMember

Hi Geraldine/GATKers :-)

I was trying to access the documentation for DepthOfCoverage from this page:

http://gatkforums.broadinstitute.org/discussion/40/using-depthofcoverage-to-find-out-how-much-sequence-data-you-have

that links to here:

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

But the link doesn't seem to be working. Could you possibly update the link so that I could take a look at the argument details?

Thank you so much as always!
Steve

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  • estif74estif74 Saint Paul, MN, USAMember

    awesome thanks!

  • estif74estif74 Saint Paul, MN, USAMember

    Hi Geraldine,

    I had one other follow-up question - am hoping this is related to a similar link issue...

    So I've noticed that none of my Queue Scala scripts work anymore when I try to call the new version of Queue (3.2-2), but they work fine when I call the 3.1-1 version.

    At the beginning of one of my Scala scripts, for example, I have the following lines:

    import org.broadinstitute.sting.queue.QScript
    import org.broadinstitute.sting.queue.extensions.gatk._
    import org.broadinstitute.sting.queue.extensions.gatk.HaplotypeCaller
    import org.broadinstitute.sting.queue.extensions.gatk.GenotypeGVCFs

    Do I need to update these links to make them work with the new version of Queue?

    I won't bore you with my entire scala script, but these are some of the error messages I'm getting:

    INFO 20:35:13,164 QScriptManager - Compiling 1 QScript
    ERROR 20:35:13,427 QScriptManager - queue_singlesample_makegvcf_2.scala:1: object sting is not a member of package org.broadinstitute
    ERROR 20:35:13,437 QScriptManager - import org.broadinstitute.sting.queue.QScript
    ERROR 20:35:13,438 QScriptManager - ^
    ERROR 20:35:13,444 QScriptManager - queue_singlesample_makegvcf_2.scala:2: object sting is not a member of package org.broadinstitute
    ERROR 20:35:13,452 QScriptManager - import org.broadinstitute.sting.queue.extensions.gatk._
    ERROR 20:35:13,453 QScriptManager - ^
    ERROR 20:35:13,456 QScriptManager - queue_singlesample_makegvcf_2.scala:3: object sting is not a member of package org.broadinstitute
    ERROR 20:35:13,463 QScriptManager - import org.broadinstitute.sting.queue.extensions.gatk.HaplotypeCaller
    ERROR 20:35:13,464 QScriptManager - ^
    ERROR 20:35:13,466 QScriptManager - queue_singlesample_makegvcf_2.scala:4: object sting is not a member of package org.broadinstitute
    ERROR 20:35:13,473 QScriptManager - import org.broadinstitute.sting.queue.extensions.gatk.GenotypeGVCFs

    Thanks!!!

  • estif74estif74 Saint Paul, MN, USAMember

    OK, sorry for not reading the version notes carefully! Thanks :-)

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