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: java.lang.NullPointerException


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    Bhanu Gandham

    Hi Nguyen Nguyen Thanh


    The issue here is possibly that your bed file needs to be ordered lexicographically, which is what GATK expects. Also can you make sure that bed file is in the same order as the fasta dictionary.

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