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

Error using liftovervcf to do hg18tohg19

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    Genevieve Brandt

    Scarlett could you try running this with the newest version of GATK(4.1.8.1) and post the error message?

    Also, you may need to find a better chain file for what you are trying to do. It looks like one of your variants is not one of the possible variants at that location. 

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