Visualtion of the results

[mJaredg]

Hello Cue Lee. I am in the pleiotropy plot step. I have a couple of questions. First, did you create a manhattan plot (in the Paper) of the pleio results directly from the output of pleio? I noticed the chr column is missing there. Second, does the preprocessing/pleio pipeline create all the major input files needed for the creation of a pleiotropy plot? For instance the sumstats.txt.gz and 1000G_SNP_CHR_BP_A1_A2_CHR1.txt. Or I would need to do this by hand

[cuelee]

Hi Jared, I'm very sorry for the late reply.

The distribution version of the pleiotropyPlot software can be a bit tricky to use. Until we improve usability enough, we will be happy to help you create a pleiotropy plots from the results of your analysis. If you are interested, please let us know via email.

Email: cuelee@snu.ac.kr

First, did you create a manhattan plot (in the Paper) of the pleio results directly from the output of pleio? -Unfortunately not. I created and used a reference that contains the information about the chr BP major / minor alleles, etc.

Second, does the preprocessing/pleio pipeline create all the major input files needed for the creation of a pleiotropy plot?

• Have you tried running the example provided? The description below is based on the files provided in the example. input.txt.gz -> ldscpreprocess.py creates it. rg.txt.gz -> ldscpreprocess creates it. sumstats.txt.gz -> You have to create it yourself. heritability.txt.gz -> You have to create it yourself. snp.txt.gz -> You have to create it yourself. features.txt.gz -> You have to create it yourself. 1000G_SNP_CHR_BP_A1_A2_CHR1.txt -> You have to create it yourself. output.txt.gz -> PLEIO analysis results can be used.