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[4] (howto) Use scatter-gather to joint call genotypes

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    Flávia Rius

    Thank you very much for all of the tutorials, they were really helpful for me to learn WDL!

    They are very easy to understand, and to follow as well. I had fun running them!

    In other to help others to apply it, I would like to add two small corrections to the GATK commands. 

    In 

    java -jar ${GATK} \
            -T GenotypeGVCFs \
            -R ${RefFasta} \
            -V ${sep=" -V " GVCFs} \
            -o ${sampleName}_rawVariants.vcf

    The flag -T is not necessary, and the flag -o need to be in uppercase (-O). Furthermore, GATK do not accept the GVCFs together in the command GenotypeGVCFs anymore. So another task is needed: CombineGVCFs. The new task is:

    task Combine GVCFs {
    input {
    File GATK
    File RefFasta
    File RefIndex
    File RefDict
    String sampleName
    Array[File] GVCFs
    }
    command {
    java -jar ${GATK} \
    CombineGVCFs \
    -R ${RefFasta} \
    -V ${sep=" -V " GVCFs} \
    -O ${sampleName}_combined_gvcfs.vcf
    }
    output {
    File bigGVCF = "${sampleName}_combined_gvcfs.vcf"
    }
    }

    And the command for GenotypeGVCFs is:

    java -jar ${GATK} \
            -T GenotypeGVCFs \
            -R ${RefFasta} \
            -V ${bigGVCF} \
            -o ${sampleName}_rawVariants.vcf

    I hope I can help other people running the tutorial with these tips.

    Thank you again!

     

    Best regards,

    Flavia

     

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