Home - ariadnacilleros/Cis-mQTL-mapping-protocol-for-methylome GitHub Wiki

Welcome to the Cis-mQTL mapping protocol for methylome wiki!
In this GitHub repository, you will find the protocol elaborated by the Immunogenetics Research Lab (IRLab) from the University of the Basque Country (UPV/EHU), to map placental cis-mQTLs using the command-line program TensorQTL. All the commands and scripts used are available in the Readme but be careful, you will need to customize some of them, mainly the Rscripts executed from RStudio and not from the command line. Also, during the pipeline, we will be creating new directories for the outputs, but you should always work from outside of them! Have a look at the diagram below.

As it is indicated in the Readme, to complete the pipeline, you need to have the following installed: R and RStudio, Plink1.9 and Plink2, TensorQTL and its dependencies, bcftools and vcftools. In case that you have already performed the HRC genotype imputation at the Michigan Server and the preprocessing of the methylome by PACEanalysis R package by A. Binder with the specified arguments in Step 2.1., you can jump to Step 2.2.

On the following diagram, you can see the protocol that we will follow: