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

Running GenomicsDBImport/CombineGVCFs on Azure leads to User Error: Illegal argument value

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2 comments

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    Martin Danner

    Solved by getting rid of the  "\" within the command section.

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    王苏苏

    hi Martin Danner,

    May I know which part of the script you delete the '\'?  delete all these '\' in the following part? 

    ~{gatk_path} --java-options "-Xmx16g -Xms16g" \

    GenomicsDBImport \

        -V ~{input_patient} \

        -V ~{input_mother} \

        -V ~{input_father} \

        --genomicsdb-workspace-path ~{output_dir} \

        --tmp-dir ~{tmp_dir} \

        -L ~{bed_file} \

        --merge-input-intervals true \

    --max-num-intervals-to-import-in-parallel 1000 \

    --verbosity DEBUG
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