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What's the right order of Mitochondrial pipeline

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    Gökalp Çelik

    HiFiona Liang

    According to the AlignAndCall.wdl file Mutect2 Calls are before all filtering and merging steps. Here is the summary of the flow from the wdl file. I hope this helps. 

      1,18: workflow AlignAndCall {
      57,3:   call AlignAndMarkDuplicates.AlignmentPipeline as AlignToMt {
      71,3:   call AlignAndMarkDuplicates.AlignmentPipeline as AlignToShiftedMt {
      85,3:   call CollectWgsMetrics {
      98,3:   call M2 as CallMt {
      98,14:   call M2 as CallMt {
      108,23:       # Everything is called except the control region.
      114,3:   call M2 as CallShiftedMt {
      114,14:   call M2 as CallShiftedMt {
      124,23:       # Everything is called except the control region.
      130,3:   call LiftoverAndCombineVcfs {
      132,21:       shifted_vcf = CallShiftedMt.raw_vcf,
      133,13:       vcf = CallMt.raw_vcf,
      141,3:   call MergeStats {
      143,23:       shifted_stats = CallShiftedMt.stats,
      144,27:       non_shifted_stats = CallMt.stats,
      150,3:   call Filter as InitialFilter {
      173,3:   call SplitMultiAllelicsAndRemoveNonPassSites {
      183,3:   call GetContamination {
      189,3:   call Filter as FilterContamination {
      216,5:     call FilterNuMTs {
      232,3:   call FilterLowHetSites {

     

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    Fiona Liang

    Hi developer,

    Thank you for your reply.

    Where can I find files(or functions) called by AlignAndCall.wdl ?

    Program files in google cloud of terra are a little bit different from AlignAndCall.wdl.

    > https://app.terra.bio/#workspaces/help-gatk/Mitochondria-SNPs-Indels-hg38

    Maybe files in terra is an old version? 

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    Gökalp Çelik

    Hi Fiona Liang

    MitochondriaPipeline  workflow in the terra workspace uses the AlignAndCall.wdl script from the following link. 

    https://github.com/broadinstitute/gatk/blob/4.1.8.0/scripts/mitochondria_m2_wdl/AlignAndCall.wdl

    I hope this helps 

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    Fiona Liang

    Hi,

    Thank you.

    I'm still confused because the terra bucket on google clould is different form AlignAndCall.wdl.

    Steps in AlignAndCall.wdl are equal to those described in gatk mitochondrial best practice.

    The following steps are not in terra bucket on google cloud:

    # https://console.cloud.google.com/storage/browser/fc-ccb0e231-7c8d-4a45-82a3-0f3584a216c0;tab=objects?authuser=0&prefix=&forceOnObjectsSortingFiltering=false
    # https://app.terra.bio/#workspaces/help-gatk/Mitochondria-SNPs-Indels-hg38
    MergeStats
    SplitMultiAllelicsAndRemoveNonPassSites
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    Gökalp Çelik

    Hi Fiona Liang

    The Mitochondria.wdl in the terra workspace imports AlignAndCall.wdl from the github repository to complete its actions therefore the order of steps is not an issue if this is really what you are worried about. Terra workspace does not explicitly show the AlignAndCall.wdl file therefore you are only faced with Mitochondria.wdl. 

    I hope this helps. 

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