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 do I run CreateExtendedIlluminaManifest myself (for GtcToVcf) for a customized Illumina chip?

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    Genevieve Brandt (she/her)

    Hi Nick Rafaels,

    Thanks for bringing up this problem so that we can look into it. This is a new PICARD tool so it looks like no documentation has been added yet. I put in a ticket at this link here: https://github.com/broadinstitute/picard/issues/1708. I tagged the developer so he can comment on how to use the REPORT_FILE argument and also add more documentation.

    You can follow along on github for more updates.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi Nick Rafaels,

    A member of the Picard team commented that they will be adding Tool Docs, so thank you for bringing this to our attention. I also wanted to let you know that the report file is an output file, so you do not need to provide anything for input with that argument.

    Hope this helps!

    Genevieve

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