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

GenomicsDB Import issues

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    Anthony Dias-Ciarla

    Hi aheritas,

    Thank you for writing to the GATK forum! We hope that we can help you sort this out.

    To start, please use the GATK tool, UpdateVCFSequenceDictionary, to re-header your vcf. You must provide a dictionary and the vcf you want to update; it will copy the dictionary into your vcf header. Ensure you run with --replace argument to ensure the original vcf gets overwritten.

    Please let us know when you’ve done the above and have rerun GenomicsDB.

    Best,

    Anthony

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