Run GISTIC, make zip file for data release

[jharenza]

This section is required for PM/ADAPT team

[Required] For what study (study_id) is this request?

OpenPedCan

[Required] Basic study information

• [x] Is this an OT or Kids First study: OT
• [ ] If KF, PI name and fiscal year:
• [ ] Study short name:

NOTE: Study short name is required for D3B study, but optional for Kids First X01; Fiscal year is required for Kids First X01, but optional for D3B study. Those information will be used for project naming in Cavatica.

[Required] What workflow needs to be done?

For reference: https://www.notion.so/d3b/workflow-type-365a604413534b2b9d93c969557d60a2

• [ ] alignment
• [ ] gatk-hc-gvcf
• [ ] family-vcf-genotyping
• [ ] cohort-vcf-genotyping
• [ ] single-vcf-genotyping
• [ ] somatic-analysis
• [ ] rnaseq-analysis
• [ ] only delivery of the source data
• [ ] rnaseq toolkit run ( this would be D3b toolkit modules like collapse RSEM files , merge RSEM files , merge fusion calls )
• [x] dnaseq toolkit run ( this would be D3b toolkit modules like consensus CNV analysis, merge consensus maf files )

Run GISTIC on OpenPedCan v11 cohort, create zip folder, place on s3 in v11 folder.

[Required] Requested sample manifest.

Please provide a description selection criteria for the samples need to be processed. E.g. "the entire study" or "all visible tumors". Along with a requested sample manifest in the format of tab delimited file with columns of biospecimen_id, experiment_strategy, source_text_tissue_type and genomics_file_id. Please attach the manifest directly to this ticket or post a downloadable link if manifest is on DataTracker.

[Required] Billing group for this study?

If there's no billing group setup for this study or project yet, please follow the D3b Billing Workflow guidelines and submit your request at D3b Billing Group Creation board

[Optional] List bucket names for source files.

[Optional] What is the priority for the analysis? (Low, Medium, High)

[Optional] How long do you think this work will take?

[Optional] Who will complete this work?

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This section is ONLY REQUIRED for Bixops manager/operations

[Required] Provide Cavatica project link.

[Required] Provide details for analysis workflow(s).

[zhangb1]

Just talked to @runjin326 ,seems the NA issue has been fixed.

I will work on the this gistic run ...

[jharenza]

thank you @zhangb1

[zhangb1]

2022-06-07 10:59:27   16727287 cnv-consensus-gistic.zip

s3://d3b-openaccess-us-east-1-prd-pbta/open-targets/v11/

Gistic file has been uploaded to the s3 bucket , let me know any issues.