Hello,

I am currently using Longshot for variant calling on my BAM file. However, I'm encountering an issue where the number of variants generated does not match the expected count. Could you advise on which parameters might be adjusted to ensure that all possible variants are generated? I plan to filter these variants in subsequent steps, but initially, I need to capture the complete set of potential variants.

Thank you for your assistance.

# Variables (these should be set to actual paths/values before running the script)
bam_path="/path/to/your/bam_file.sorted.bam"
ref_genome="/path/to/your/reference_genome.fa"
output_vcf="/path/to/output_directory/output_filename.vcf"

# Run Longshot with specified parameters
longshot \
  --bam "$bam_path" \
  --ref "$ref_genome" \
  --out "$output_vcf" \
  --min_cov 1 \
  --min_mapq 1 \
  --min_allele_qual 1