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The Pipelines
Scott.Hazelhurst edited this page May 26, 2017
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There four pipelines that are available, which may be run independently.
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affy-call.nf
This piplines takes raw Affmetrix CEL files and produces PLINK files. This is discussed here Affy Calling
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topbottom.nf
This pipeline takes raw calls provided in Illumina TOP/BOTTOM format and converts to PLINK.
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plink-qc.nf
This is the main pipeline and does quality control for the GWAS. This is diussed here PLINK QC pipeline
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plink-assoc.nf
This does a preliminary association study that can be used as a starting point for more rigorous analysis. This is discussed here Association testing pipeline
These are discussed below in subsequent section.
About h3aGWAS
Getting started
Running pipelines
- Quick Start
- The nextflow config file
- Pipeline options
- The Pipelines
- Affy Calling
- Converting from Illumina Top-Bottom
- PLINK QC pipeline
- Association testing pipeline
- Post-GWAS analysis
Extending pipelines
Getting help