GATK SV required inputs

Edited July 15, 2022 16:12
10 comments

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

10 comments

Josh Evans
- July 15, 2022 18:39
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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Edward C
- July 15, 2022 19:55
Hi Josh,

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

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Josh Evans
- July 15, 2022 19:57
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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Edward C
- July 15, 2022 19:59
https://app.terra.bio/#workspaces/workshop-BroadE-2206/GATK-Structural-Variants-Single-Sample_RC_07122022

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Josh Evans
- July 15, 2022 20:03
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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Josh Evans
- July 18, 2022 14:41
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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Melissa Nel
- August 24, 2022 09:10
Hi. I am having the same issue when trying to run this workflow. I have cloned the featured workspace and added my samples under the data tab. When I click on gatk-sv-single-sample to launch the workflow and select the latest v0.24.1-beta version it flags missing input data including the fields mentioned by Edward C on this thread.

Chris Whelan Mark Walker, how do I get these fields to auto-populate? Am I using the correct workflow version?

Thanks for the assistance,

Melissa

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Shoaib Rakhangi
- August 24, 2022 20:03
Hi Melissa,

Sorry to hear that you are having issues running workflows! The workflow page for gatk-sv-single-sample has the version set to v0.12-beta by default. Try running that version and seeing if you still run into input issues.

Kind regards,
Shoaib

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Shoaib Rakhangi
- August 29, 2022 19:45
Hi Melissa,

We haven't heard from you in a while! Have you managed to get your workflow running with no issues?

Kind regards,
Shoaib

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Shoaib Rakhangi
- September 06, 2022 17:44
Hi Melissa,

We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this post and we'll be happy to pick up where we left off!

Kind regards,
Shoaib

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