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[1] (howto) Write your first WDL script running GATK HaplotypeCaller




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    Michael Apostolides

    GATK has been updated to GATK4. It should be noted that "GenomeAnalysisTK.jar" file no longer exists in this version.

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    Michael Apostolides

    As an added note, the gatk command should look like this, with the corresponding GATK4 syntax changes:

       java -jar ${GATK} HaplotypeCaller \

            -R ${RefFasta} \

            -I ${inputBAM} \

            -O ${sampleName}.raw.indels.snps.vcf


    Additionally, the .jar file used in the .json file will differ as such:

    "gatk-package-" should be used instead of "GenomeAnalysisTK.jar"


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