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c-BIG / NPM-sample-qc

reference implementation of GA4GH WGS Quality Control Standards
https://c-big.github.io/NPM-sample-qc
MIT License
9 stars 3 forks source link

Add metric to estimate cross contamination rate #88

Closed justinjj24 closed 1 year ago

justinjj24 commented 1 year ago

Include metric cross contamination rate using verifybamid2 same settings as All Of Us QC Report doc

https://sg-npm.atlassian.net/jira/software/projects/SQC/boards/12?selectedIssue=SQC-62

Need bigger data to run unittest, the current data NA12878-chr14-AKT1 failed to run by verifybamid

justinjj24 commented 1 year ago

Implemented and test run with NA12878... PR-https://github.com/c-BIG/NPM-sample-qc/pull/90

Need bigger data to run unittest, the current input data NA12878-chr14-AKT1.bam not sufficient to run verifybamid. Alternative data for unittest?

justinjj24 commented 1 year ago

Added errorStrategy 'ignore' to prevent workflow failure