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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

FASTA - Reference genome format Follow


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    Field -Ye Tian

    Dear GATK group,

    I was trying to build a sequence dictionary file for the grch38 assembly downloaded from NCBI.

    I first tried the 

    gatk-launch CreateSequenceDictionary -R ref.fasta 

    command, where I was told "gatk-launch" can't be found. 

    Instintively I tried without the -launch, this time the program CreateSequenceDictionary mode can be loaded but I encountered an error says, 

    Illegal argument value: Positional arguments were provided ',/home/field/shared/Genome_Refs/GCF_000001405.26_GRCh38_genomic.fna}' but no positional argument is defined for this tool.

    I searched but failed to find a solution.





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  • Avatar
    Field -Ye Tian

    I have later on figured out that the dictionary can also be generated with the Picard-tools with the command

    java -jar picard.jar CreateSequenceDictionary \ 
    R=reference.fasta \


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  • Avatar
    Siyuan Feng

    As mentioned by @Field -Ye Tian, "gatk-launch" can't be found with an normal version of GATK (in my case is GATK 3.8). Also it's not mentioned in '--help' stdout or GATK user's manual. Lucky that we still have the option to use CreateSequenceDictionary in Picard.

    Thus, I'm wondering whether the "gatk-launch" module is an independent module from the GATK jar file, or it has already been removed from the GATK main program?

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    Layne Sadler

    The page in this error message does not exist

    A USER ERROR has occurred: Fasta index file ...
    Please see for help creating it.

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