samtools mpileup description
Samtools mpileup generates BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample identifiers in RG header lines. If sample identifiers are absent, each input file is regarded as one sample.
Parent program: samtools
SAMTools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. It is very convinient for handling reads mapped to reference genome. Normally SAMtools is used in intermediate step between raw read mapping and SNP or variants callingm, because it allows to effeciently store mapped reads.