Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more


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    James Emery

    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: (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: as the pileup-calling code that was part of the Microbes branch has finally been merged into the codebase. 

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    Jian Wang

    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?



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    Gökalp Çelik

    Hi Jian Wang

    ShiftFasta is already available in the latest GATK 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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