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

GenomeSTRiP SVGenotyping script and alt allele alignment

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    Bhanu Gandham

    Hi Thandeka

     

    I am adding Bob Handsaker to this thread. Bob will be able to help you out with this.

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    Bob Handsaker

    I recommend no longer running alt allele alignment. Just skip this step and the -altAlignments argument.

    By the way, the best practices are to follow the WDLs, not the installtest script.

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    Thandeka

    Hi Bob, thank you for the response, I'm sorry but what is  WDLs? will WDLs also help me with the CNVDiscovery?

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    Bob Handsaker

    WDL is a workflow description language used by terra and similar tools/environments https://app.terra.bio/

    The WDLs we use to run Genome STRiP are in the wdl directory (wdl/firecloud).

     

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