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samtools mpileup

By Li H., Durbin R., Last update 1494698999
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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.