05_regenie_step1.bsub

#!/bin/bash
#BSUB -q long                            #Set you submission
#BSUB -J regenie_step1_LM                #Name of the job
#BSUB -n 32                              #Request 32 cores
#BSUB -R "span[ptile=32]"                #Request 8 cores per node.
#BSUB -R "rusage[mem=8GB]"               #Request 8GB per core for the job
#BSUB -o /your/out/dir/rg_step1_LM.out   #Give path for the out file
#BSUB -e /your/err/dir/rg_step1_LM.err   #Give path for the err file


#Load modules
module load regenie/3.2.2

#Regenie step1
regenie \
  --step 1 \
  --bed ukb_cal_allChrs \
  --extract qc_pass.snplist \
  --keep qc_pass.id \
  --phenoFile ukb_phenotypes_LM.txt \
  --covarFile ukb_covariates_LM.txt \
  --bt \
  --bsize 1000 \
  --lowmem \
  --out ukb_step1_LM