The GWAS analysis type#

The gwas-norm pipeline, implement a number of analysis types. An analyses type is high level information about the type of phenotype being investigated. These do not influence the normalisation directly but are incorporated into the output normalised file.

The following analyses types are available:

  • hqtl - A histone QTL analysis type, i.e. a GWAS if variants influencing histone modifications

  • pqtl - A protein quantitative trait type, i.e. a GWAS of variants influencing protein values or activities.

  • eqtl - An expression quantitative trait type, i.e. a GWAS of variants influencing transcript values.

  • sqtl - A splicing quantitative trait type, i.e. a GWAS of variants influencing values of differentially spliced transcripts.

  • mqtl - A methylation quantitative trait type, i.e. a GWAS of variants different methylation signatures.

  • metabqtl - A metabolite quantitative trait type, i.e. a GWAS of variants influencing metabolite biomarker levels such as LDL-C.

  • qtl - A general quantitative trait type that is not covered by the molecular QTL trait types, i.e. blood pressure , height or BMI.

  • disease - A disease trait type, i.e. a GWAS of variants influencing type 2 diabetes.

  • trait - A general trait type that is not covered by anything else above.

Please let me know if you want any analysis types added, it is very easy to do.