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

HaplotypeCaller -ERC GVCF -variant_index_type LINEAR


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    Bhanu Gandham

    Hi Matilde


    You are using a very old version of GATK which we do not support anymore. Please upgrade to the latest version of GATK v The latest version of GATK does not require "-variant_index_type" argument anymore. That was a temporary workaround for an issue with index compression in a very old version of GATK.

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