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question about flowcell_unmapped_bams_list ?

jin0008jin0008 Seoul, South KoreaMember

I want to run 3 samples of WGS.
I prepared uBAM files from fastq.
However, I can't go further due to absence of flowcell_unmapped_bams_list file.
How can I make this from uBAM or fastq?

Best Answer


  • buchnerdbuchnerd CWRUMember

    I'm trying to run the Method "gatk/pre-processing-hg38-gatk4" and I have the same question about what is supposed to go into the flowcell_unmapped_bams_list file. I'm getting the error message "PairedEndSingleSampleWorkflow.flowcell_unmapped_bams_list -
    Expected single value for workflow input, but evaluated result set was empty" but I couldn't figure out how to fix the error from the other thread referred to above. Any suggestions?? Thanks!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @buchnerd Looking into this right now and will get back to you soon!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin
    edited December 2018

    @buchnerd The flowcell_unmapped_bams_list is just a list of input ubam files from a single sample. “One or more read groups, one per uBAM file, all belonging to a single sample (SM)” as listed in the WDL requirements! The format of what this should look like can be found in this link of the json file. This list is essentially used to scatter and align the input bam files in parallel. Let us know if this helps!

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