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

CreateSomaticPanelOfNormals fails



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    Bhanu Gandham

    Hi Dieter Best

    1. Looks like one of the input vcfs in your normals.list is not sorted. Can you check for that please?
    2. If the above is not the issue then how were the vcfs produced? Mutect2 should not produce unsorted vcf.  If you are using Mutect2 to produce these vcfs then please provide pipeline you are using



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    Dieter Best

    Thanks for responding so quickly.

    The bam files were produced with Mutect2 from GATK version

    The vcf files are in fact NOT sorted.

    I solved the problem with "picard SortVcf".



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