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Yan Holtz, Zhihong Zhu, Julanne Frater, Perry Bartlett, Jian Yang, John McGrath

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Abstract:

Data analysis: this document summarizes the data analysis leading to the results presented in the paper. It is organized as follow:

• GWAS description: a quick description of the vitamin-D GWAS result that is the basis of the mendelian randomization pipeline.
• GSMR: description of the GSMR pipeline to find out if Vitamin-D has a causal effect on several mental diseases.
• LDSC: usage of LD score regression to assess heritability and genetic correlation with other traits.
• mtCOJO: usage of the mtCOJO method to test the putative confounding effect of other risk factors.

Note: Some of the script described here are computationnaly intensive and thus run on 2 different clusters. See the code below for connection on the cluster.

# ------  DELTA -----------
ssh y.holtz@delta.imb.uq.edu.au
cd /shares/compbio/Group-Wray/YanHoltz/

# Medici on delta:
cd /gpfs/gpfs01/polaris/Q0286/

# ------  INODE -----------
ssh uqyholtz@inode.qbi.uq.edu.au
/ibscratch/wrayvisscher/Yan_Holtz/

Note: This document is hosted in this github repository

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A work by Yan Holtz

Yan.holtz.data@gmail.com