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.

#!/bin/bash
p=$1

dependencies="afterok"
while read pheno; do
if [ -n "${pheno}" ]; then
  job = `( sbatch -o $p/sbatch_logs/chr0.$pheno.%j.out ./bin/model_eval_cv_genotyped.sh $p $pheno | cut -f 4 -d ' ' )`
  dependencies+=:$job
fi
done < $p/phenotypes.txt

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

# Run for each chromosome/chunk
dependencies="afterok"
for chr in {1..22} {101..112};do
  job = `(sbatch -N 1 -n 1 -o $p/sbatch_logs/chr${chr}.cv.%j.out ./bin/rotroff_scripts/model_eval_cv_imputed.sh $p $chr | cut -f 1 -d ' ')`
  dependencies+=:$job
done

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