My little slurm script gives me very low number of variant. Please suggest how to improve my GATK script to catch all variants

#!/bin/bash
#@(#)GATK_4.50-slurm_bioconda3_rns.sh  2024-05-15  R.N.Sarma

## #SBATCH -n 8 instead of 4 CPU 2027-05-27 R.N.Sarma

## The main script was submitted prefixed sbatch -w brahma to ensure jobs are submitted to the node brahma 2027-05-27 R.N.Sarma

## Added "StandardAnnotation", "min/max-alleles 2" and "EMIT_ALL_CONFIDENT_SITES" in the code.

# Path to the reference genome
reference="/home/rnsarma/Desktop/Mungbean/mungbean_genome/Vigna_radiata.Vradiata_ver6.dna.toplevel.fa"

# Output VCF file
output_vcf="../raw_variants_mungbean_new_slurm_1.vcf"

# Temporary directory
tmp_dir="/var/tmp" 

# Directory containing *.sorted.bam files
input_directory="/home/rnsarma/Desktop/Mungbean/mapping_new_bioconda_3" 

# Output directory
OUTPUT="GATK_4.50-slurm_bioconda3_rns"
mkdir -p "$OUTPUT" || { echo "Error: Failed to create output directory."; exit 1; }
cd "$OUTPUT" || { echo "Error: Failed to change directory."; exit 1; }

# Make a list of samples for loop
# The list is created based on file names in the directory
if [ ! -d "$input_directory" ]; then
 echo "Error: Input directory '$input_directory' does not exist."
 exit 1
fi

(cd $input_directory; ls) | grep -E '^([^.]+)\.' | sed 's/\.[^.]*$//' > Samplelist.$$

# Check if the sample list file exists
sample_list="Samplelist.$$"
if [[ ! -f $sample_list ]]; then
  echo "Error: Sample list file $sample_list not found."
  exit 1
fi

# Initialize an array to hold Slurm job IDs
declare -a JOB_IDS

# Submit one sbatch job per sample
while IFS= read -r i; do
    cat <<EOF > main_script.sh
#!/bin/bash
#SBATCH --mem=64G

# Run in (gbs) bioconda3 environment
source /usr/local/bin/bioconda3.rc
conda activate gbs

# Change directory to the input directory
cd "$input_directory" || { echo "Error: Failed to change directory."; exit 1; }

# Create an array to store the file paths
declare -a input_files

# Read *.sorted.bam file paths and append them with "-I" flag
for file in *.sorted.bam; do
    input_files+=("-I" "\$file")
done

# Construct the command array
command_args=("gatk" "HaplotypeCaller" "-R" "$reference")
command_args+=("\${input_files[@]}")
command_args+=("-O" "$output_vcf" "-G" "StandardAnnotation"  "--output-mode" "EMIT_ALL_CONFIDENT_SITES" "--tmp-dir" "$tmp_dir")

# Print the command
echo "\${command_args[@]}"
# Run the command
"\${command_args[@]}"
EOF

    # Submit the main Slurm job script
    sbatch main_script.sh
done < "$sample_list"

# Clean up temporary files
rm "$sample_list" main_script.sh

# Print a message indicating job submission
echo "Submitted job for generating the VCF file: $output_vcf"