sh [SMR]基于概要的孟德尔随机化

Posted 2021-05-07

smr=/u/home/g/gandalm/project-gandalm/SMR/smr_Linux

bfile=/u/home/g/gandalm/nobackup-dhg/PsychEncodeGenotypes/PsychEncode

gwas=/u/home/g/gandalm/project-gandalm/datasets/GWAS/SCZ.CLOZUK.2018/SCZ.CLOZUK.2018.COJO.chrBP.ma

eqtl=/u/home/g/gandalm/project-gandalm/datasets/eQTL/PsychEncode/PsychEncode_eQTL

MHCsnps=/u/home/g/gandalm/project-gandalm/datasets/GWAS/MHC_snps.list

#fdrSignSNPS=/u/home/g/gandalm/project-gandalm/datasets/eQTL/PsychEncode/isoQTL_significant_snps.list

$smr --bfile $bfile --gwas-summary $gwas --beqtl-summary $eqtl --out ./output/SCZ_eQTL_noMHC_trans --thread-num 16 --smr-multi --exclude-snp $MHCsnps --trans 


source("plot_SMR.r")
SMRData = ReadSMRData("./plot/SCZ_isoQTL_sigOnly_noMHC.ENST00000242152.2.txt")
SMRLocusPlot(data=SMRData, smr_thresh=8.4e-6, heidi_thresh=0.05, plotWindow=2000, max_anno_probe=16)