GATK SV required inputs

Post author
Edward C

Hi Chris Whelan! I'm trying to run GATK SV on a single WGS sample and would like to know what the recommended values are for the following required inputs. Thanks!

annotation_max_shards_per_chrom_step1
annotation_min_records_per_shard_step1
clean_vcf1b_records_per_shard
clean_vcf5_records_per_shard
max_shard_size_resolve

Comments

6 comments

  • Comment author
    Josh Evans

    Hi Edward,

    Thanks for writing in! If you provide me with a link to the workflow you're using or the Featured Workspace, I'd be happy to see if I can determine the answer to your question.

    Please let me know if you have any questions.

    Best,

    Josh

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  • Comment author
    Edward C

    Hi Josh,

    I just shared the workspace with Support. Are you able to see it now?

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  • Comment author
    Josh Evans

    Hi Edward,

    Thanks for getting back to us! Can you please provide a link to the workspace, so that we can locate it in the system? Once we have that, we'll take a look as soon as we can.  Also, what's the name of the workflow, just to confirm?

    Thanks,

    Josh

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  • Comment author
    Edward C

    https://app.terra.bio/#workspaces/workshop-BroadE-2206/GATK-Structural-Variants-Single-Sample_RC_07122022

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  • Comment author
    Josh Evans

    Hi Edward,

    Thanks for the link, I'll take a look at the workflow and see if I can find answer to your question as soon as I can. 

    Best,

    Josh

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  • Comment author
    Josh Evans

    Hi Edward,

    I had our GATK support team take a look at your question, and they noticed that the version of the workspace and workflow you're running is the BroadE version.  They suggested running the workflow from our Featured Workspace as it doesn't have those inputs listed above and will make running everything more streamlined.  You can find the featured workspace here.

    Please let me know if that's helpful for you or if you have any questions.

    Best,

    Josh

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