samtools

samtools sort

samtools sort

Version:
1.x
Identifier: TL_ec2a8d_ca.0b
Tool

Description


samtools sort [-l level] [-m maxMem] [-o out.bam] [-O format] [-n] [-t tag] [-T tmpprefix] [-@ threads] [in.sam|in.bam|in.cram] Sort alignments by leftmost coordinates, or by read name when -n is used. An appropriate @HD-SO sort order header tag will be added or an existing one updated if necessary. The sorted output is written to standard output by default, or to the specified file (out.bam) when -o is used. This command will also create temporary files tmpprefix.%d.bam as needed when the entire alignment data cannot fit into memory (as controlled via the -m option). Consider using samtools collate instead if you need name collated data without a full lexicographical sort.

Author(s)

  • Heng Li
  • Bob Handsaker
  • Jue Ruan
  • Colin Hercus
  • Petr Danecek

Code Repository

  • GitHub

    https://github.com/samtools/samtools

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