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 get error, but VCF get indexed


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    Bhanu Gandham



    1. Is the index file empty?

    2. Please always use exit code to determine if a GATK tool ran successfully or not. If the GATK errors out it will exit with a non-0 status code. You can check the exit code manually in the shell or in your script, eg., in bash it would be $?

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