The Pipelines

There four pipelines that are available, which may be run independently.

• affy-call.nf

  This piplines takes raw Affmetrix CEL files and produces PLINK files. This is discussed here Affy Calling

• topbottom.nf

  This pipeline takes raw calls provided in Illumina TOP/BOTTOM format and converts to PLINK.

• plink-qc.nf

  This is the main pipeline and does quality control for the GWAS. This is diussed here PLINK QC pipeline

• 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.