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

Hi, I am new to GATK trying to call variants from WGS and I am getting the below error. What could be the issue



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    Gökalp Çelik

    Hi Ademola Aina

    GATK tools require presence of a sequence dictionary file next to the fasta file you use in your -R parameter. If it is not present or is present but not compatible or corrupt you may generate one using 

    gatk CreateSequenceDictionary



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    Ademola Aina

    Thanks. I just re-ran the same gatk CreatSequenceDictionary line I had before and it worked just fine.

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