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NCI-CGR / GwasQcPipeline

The CGR GWAS QC processing workflow.
https://nci-cgr.github.io/GwasQcPipeline/
MIT License
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Option to run the QC pipeline with GTC files only (without the idat files) #247

Open liuj1818 opened 1 year ago

liuj1818 commented 1 year ago

We would like the option to be able to run the GWAS QC pipeline with GTC files only (when the .idat files are not available). Basically, the pipeline skips the intensity check and the contamination check and runs the remaining QC checks.