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

(How to) Install all software packages required to follow the GATK Best Practices Follow


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    Jongwon Lee

    Thank you for valuable information.

    I'm being helped a lot about BI tools.

    There are missed head number on [2. SAMtools] :)

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    Chrsitopher Eskiw

    Sorry for the naive question here but do these installations need to performed within the Docker container or are they independent?

    I am having issues installing BWA.



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    I think there is a typo in this page. 

    Some .zip files are using tar with 'j' option and .bz2 files are using 'z' option when it has to be the other way around - xvzf for zip files and xvjf for bz2 files. You might want to correct this as trying to extract with the wrong flags will throw an error.

    Thank you.

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