This protocol step involves variant calling and single nucleotide polymorphism (SNP) generation using SAMtools mpileup and BCFtools call. The SAMtools mpileup command is used to generate a pileup format file from multiple BAM files aligned to a reference genome. This file contains information about the alignment of sequencing reads to the reference genome at each genomic position. The BCFtools call command then analyzes the pileup data to identify variants, including SNPs, insertions, deletions, and complex variants. The output is generated in variant call format (VCF), providing detailed information about the detected variants, including their genomic coordinates, allele frequencies, and quality scores. This protocol step is crucial for identifying genetic variations and understanding the genomic landscape of the samples under investigation.