manhattan.sb

#!/bin/bash

#SBATCH --ntasks=1
#SBATCH --job-name=Manhattan
#SBATCH --time=8:00:00
#SBATCH --cpus-per-task=8
#SBATCH --partition=short
#SBATCH --array=1-92
#SBATCH --output=work/manhattan_%A_%a.out
#SBATCH --error=work/manhattan_%A_%a.err
#SBATCH --export ALL

. /etc/profile.d/modules.sh
module load default-cardio
module load slurm
module load use.own

export p=$(cut -f1 manhattan.list | awk 'NR==ENVIRON["SLURM_ARRAY_TASK_ID"]')
export TMPDIR=/scratch/jhz22/tmp
export rt=$HOME/INF/METAL

echo ${p}
export protein=${p};
R --no-save -q <<END
    protein <- Sys.getenv("protein");
    print(protein);
    gz <- gzfile(paste0("/home/jhz22/INF/sumstats/INTERVAL/INTERVAL.",protein,".gz"));
    .libPaths("/home/jhz22/R:/home/jhz22/R-3.5.3/library")
    library(qqman,lib.loc="/home/jhz22/R");
    tbl <- read.delim(gz,as.is=TRUE);
    tbl <- within(tbl,{
       SNP <- SNPID
       CHR <- as.numeric(CHR)
       BP <- as.numeric(POS)
       P <- as.numeric(PVAL)
     })
     tbl <- subset(tbl,!is.na(CHR)&!is.na(BP)&!is.na(P))
     manhattan <- paste0("INTERVAL.",protein,".manhattan.png");
     png(manhattan,width=12,height=10,units="in",pointsize=4,res=300)
     manhattan(tbl,main=protein,genomewideline=-log10(5e-10),cex=0.8, col=c("blue","orange"),suggestiveline=FALSE,ylim=c(0,25));
     dev.off();
END