gatk-microbialmode.jar

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Jian Wang

• March 23, 2023 21:33

Can some one share a link to download gatk-microbialmode.jar?

Thanks

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  James Emery

  • April 03, 2023 17:24

  Hello Jian Wang. It appears the microbial mode jar was a branch off of gatk involving some extra code features that were implemented for the gatk-for-microbes pipeline. You should be able to find the jar posted somewehre in the associated terra workspace here: https://app.terra.bio/#workspaces/help-gatk/GATK%20For%20Microbes. (you should be able to find it in the workflow wdl on that page). 
  
  However I would recommend trying your luck running with the most recent version of the master branch in GATK here: https://github.com/broadinstitute/gatk. as the pileup-calling code that was part of the Microbes branch has finally been merged into the codebase. 

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  Skyler

  • April 07, 2023 22:46

  Here's the URL to the Google Cloud storage folder that holds the GATK for microbes files (gs://) 

  https://console.cloud.google.com/storage/browser/gatk-best-practices/gatk-for-microbes;tab=objects?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false 

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  Jian Wang

  • September 18, 2023 15:04

  Hi James,

  Thanks for your reply. I have another question for running the pipeline. I got a Error

  "A USER ERROR has occurred: 'ShiftFasta' is not a valid command.

  It seems the ShiftFasta function is not in the Jar Env.

  Could you help me fix it?

   

  Jian

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  Gökalp Çelik

  • September 18, 2023 15:12

  Hi Jian Wang

  ShiftFasta is already available in the latest GATK 4.4.0.0 as a beta tool. Could you check this version?

  --------------------------------------------------------------------------------------
  Reference:                                       Tools that analyze and manipulate FASTA format references
      BaitDesigner (Picard)                        Designs oligonucleotide baits for hybrid selection reactions.
      BwaMemIndexImageCreator                      Create a BWA-MEM index image file for use with GATK BWA tools
      CheckReferenceCompatibility                  (EXPERIMENTAL Tool) Check a BAM/VCF for compatibility against specified references.
      CompareReferences                            (EXPERIMENTAL Tool) Display reference comparison as a tab-delimited table and summarize reference differences.
      ComposeSTRTableFile                          Composes a genome-wide STR location table used for DragSTR model auto-calibration
      CountBasesInReference                        Count the numbers of each base in a reference file
      CreateSequenceDictionary (Picard)            Creates a sequence dictionary for a reference sequence.  
      ExtractSequences (Picard)                    Subsets intervals from a reference sequence to a new FASTA file.
      FastaAlternateReferenceMaker                 Create an alternative reference by combining a fasta with a vcf.
      FastaReferenceMaker                          Create snippets of a fasta file
      FindBadGenomicKmersSpark                     (BETA Tool) Identifies sequences that occur at high frequency in a reference
      NonNFastaSize (Picard)                       Counts the number of non-N bases in a fasta file.
      NormalizeFasta (Picard)                      Normalizes lines of sequence in a FASTA file to be of the same length.
      ScatterIntervalsByNs (Picard)                Writes an interval list created by splitting a reference at Ns.
      ShiftFasta                                   (BETA Tool) Creates a shifted fasta file and shift_back file
  --------------------------------------------------------------------------------------

   

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