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samtools sort

By Li H., Durbin R., Last update 1494698999
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samtools sort description

Samtools sort sorts alignments by leftmost coordinates. File .bam will be created. This command may also create temporary files .d.bam when the whole alignment cannot be fitted into memory (controlled by option -m).

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.