Plots using GWAS and eQTL datasets with locuszoom
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0
Entering edit mode
9.4 years ago
NB ▴ 960

Does anyone know how to include two datasets in locuszoom ? Something like this? On the locuszoom documentation for the standalone program, it doesn't really tell you how to go about two datasets. The command I am trying to use is

locuszoom \
  --metal file fineMap=GWASeQTL\
  --markercol SNP \
  --pvalcol P \
  --delim tab \
  --refgene Gene1 \
  --flank 500kb \
  --pop EUR \
  --build hg19 \
  --source 1000G_March2012

where, file looks like this

SNP P
SNP1 0.1
SNP1 0.3
SNP2 0.2
SNP3 0.25

and GWASeQTL looks like this

snp   chr  pos   pp  group  color
SNP1  1    1000  0.1 eQTL   red
SNP1  1    1000  0.3 GWAS   blue
SNP2  12   1153  0.2 eQTL   red

Anyone does this before?

GWAS eQTL locuszoom plots • 3.2k views
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0
Entering edit mode
5.0 years ago
Phoenix Mu ▴ 100

I think for Figure 2 in the paper you linked, it cannot be done by LocusZoom. The author did not do that, obviously.

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