Data release 8.0 - data QC

[lindaxiang]

Need to QC the process data from MUTO, POG and P1000

• MUTO QC report: https://github.com/icgc-argo/workflow-roadmap/issues/391
• POG QC report: https://github.com/icgc-argo/workflow-roadmap/issues/422
• P1000 QC report: https://github.com/icgc-argo/workflow-roadmap/issues/423

Expected output:

• compile the list of donors, analysis, and objects to be released for DR8.0

[lindaxiang]

Processed genomic data release criteria:

analysis workflow	QC criteria	analysisType	file access
dna alignment	1. must have mutect2 or sanger called successfully 2. normal coverage > 25X, tumour coverage > 30X (use column normal/tumour_estimated_coverage) 3. donors with multiple tumour/normal pairs must have all samples processed	squencing_alignment, qc_metrics	controlled
sanger variant calling	1. exclude ASCAT failed donors 2. exclude purity < 30% donors 3. exclude purity=100% donors	variant_calling, qc_metrics	controlled
mutect2 variant calling	1. cross_sample_contamination <4% (use column normal/tumour_mutect2_contamination)	variant_calling, qc_metrics	controlled

[edsu7]

Results of QC + Notes per columns updated_DR8.2024-03-04.qc.xlsx

Summary of results of DR8 ready files (excluding indices):

study	objects	donors	analyses
MUTO-INTL	15123	448	4882
P1000-US	2814	67	469
Total	17937	515	5351

Summary of results of DR8 ready files (including indices):

study	objects	donors	analyses
MUTO-INTL	18091	448	4882
P1000-US	3082	67	469
Total	21173	515	5351

List of objectIds,donorIds and analysisIds REVISED_DR8_2024-03-04.qc_files.xls

• Revised, previous version included Sanger calls that did not meet critieria

~[DR8_2024-03-04.qc_files.xlsx] (https://github.com/icgc-argo/workflow-roadmap/files/14487769/DR8_2024-03-04.qc_files.xlsx)~

[justincorrigible]

Closing as completed 👍