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Illumina ICE interval list

Hi! I am using the Featured/Best practices workspace Somatic-SNVs-Indels-GATK4 to analyze WES samples. My samples were analyzed using Illumina's ICE exome capture kit, and I have a list of intervals (attached). I am wondering whether the "workspace.intervals" attribute in method configurations of this workspace already includes this Illumina ICE exome interval list, and if not, how do I upload this interval list into my method configuration as an attribute?

Thanks!!

Best Answer

Answers

  • aboyntonaboynton Member

    Thank you!!

    So yeah yesterday I went ahead and uploaded that ICE interval list I attached above into the google bucket for my workspace, and provided the link to it as the attribute. I compared the results to just using "workspace.intervals" and they're very similar with just some minor differences. Thanks for your help!

    Adam

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    @aboynton I am glad that worked!

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