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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 Member admin

    @aboynton I am glad that worked!

  • Angry_PandaAngry_Panda Member

    @AdelaideR said:
    @aboynton - I believe it is the same, it matches the Broad protocol for generating WES samples, which incorporates the Illumina ICE exome capture kit as well. The product sheet can be found here

    If you want to make absolutely sure, you may input a different interval file using -L and providing an absolute path to the file. [google bucket in the workspace]

    Or you could replace the attribute in your json file for your workflow.

    The default in the json is:

    "Mutect2_Panel.intervals": "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",

    You could replace this with a path to your interval list in your workspace.

    Is that enough information to get you started?

    Hi @AdelaideR , I want to do the same thing locally with my own 24 cores VM. I downloaded this list, stored locally and gave its absolute path in the json file. However, should I adjust the list "UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta" ?

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited August 5

    Hi @Angry_Panda

    As this is a WDL related question I am going to pass this on to the WDL team and someone will get back to you shortly.

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @Angry_Panda Are you asking about adjusting the path to the fasta file or are you asking about physically modifying the fasta reference>

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