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

WDL RNA-seq Hisat2


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    Jason Cerrato

    Hi Thinh B. Vo,

    Thank you for writing in. Unfortunately we do not support the function of hisat2 as it is not one of our GATK tools. I've also heard of other users having trouble getting hisat2 working, but they seem to have more success using bowtie2.

    If we can be of any further assistance for GATK-related issues, please let us know and we'll be happy to help!

    Kind regards,


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