Using sbatch or srun you can make the start of your job dependent on the successful completion (or failure) of a prior job. This could be useful if you have some data preparation to do, followed by your analysis.

This code uses srun -d afterok:NNNNN to wait for some jobs submitted using sbatch to complete.

#!/bin/bash

dependencies="afterok"
while read pheno; do
if [ -n "${pheno}" ]; then
  job = `( sbatch -o $pheno.%j.out prepare_pheno $p $pheno | cut -f 4 -d ' ' )`
  dependencies+=:$job
fi
done < phenotypes.txt

# Wait for these jobs to complete (trick)
srun -d $dependencies echo "All phenotype preparation done"

# Run for each chromosome
dependencies="afterok"
for chr in {1..22}; do
  job = `(sbatch -o chr${chr}.%j.out run_model.sh $p $chr | cut -f 1 -d ' ')`
  dependencies+=:$job
done

# Wait for these jobs to complete (trick)
srun -d $dependencies echo "All analyses done"

# Do more stuff...