emagma_Amygdala_script

##eMAGMA tutorial
##Angela Mina Vargas 09112019

###############Gene-based eMAGMA!############

./magma --bfile g1000_eur --gene-annot Brain/Brain_Amygdala.genes.annot --pval MDD2018_ex23andMe_emagma2.txt ncol=Neff --gene-settings adap-permp=10000 --out Amygdala_emagma

###########Select significant genes!##########

awk '{if ($9<=3.8431e-5) print $0}' Amygdala_emagma.genes.out > Amygdala_signif_genes.txt


################GENE-sets networks analysis!#########


./magma --gene-results Amygdala_emagma.genes.raw --set-annot network_files/Brain_Amygdala_entrez_gtex_v7_normalised.txt col=2,1 --out Amygdala_emagma