samtools-sort - Man Page

sorts SAM/BAM/CRAM files

Synopsis

samtools sort [-l level] [-u] [-m maxMem] [-o out.bam] [-O format] [-M] [-K kmerLen] [-n] [-t tag] [-T tmpprefix] [-@ threads] [in.sam|in.bam|in.cram]

Description

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.

Note that if the sorted output file is to be indexed with samtools index, the default coordinate sort must be used. Thus the -n and -t options are incompatible with samtools index.

Options

-K INT

Sets the kmer size to be used in the -M option. [20]

-l INT

Set the desired compression level for the final output file, ranging from 0 (uncompressed) or 1 (fastest but minimal compression) to 9 (best compression but slowest to write), similarly to gzip(1)'s compression level setting.

If -l is not used, the default compression level will apply.

-u

Set the compression level to 0, for uncompressed output.  This is a synonym for -l 0.

-m INT

Approximately the maximum required memory per thread, specified either in bytes or with a K, M, or G suffix. [768 MiB]

To prevent sort from creating a huge number of temporary files, it enforces a minimum value of 1M for this setting.

-M

Sort unmapped reads (those in chromosome "*") by their sequence minimiser (Schleimer et al., 2003; Roberts et al., 2004), also reverse complementing as appropriate.  This has the effect of collating some similar data together, improving the compressibility of the unmapped sequence.  The minimiser kmer size is adjusted using the -K option.  Note data compressed in this manner may need to be name collated prior to conversion back to fastq.

Mapped sequences are sorted by chromosome and position.

-n

Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates.

-t TAG

Sort first by the value in the alignment tag TAG, then by position or name (if also using -n).

-o FILE

Write the final sorted output to FILE, rather than to standard output.

-O FORMAT

Write the final output as sam, bam, or cram.

By default, samtools tries to select a format based on the -o filename extension; if output is to standard output or no format can be deduced, bam is selected.

-T PREFIX

Write temporary files to PREFIX.nnnn.bam, or if the specified PREFIX is an existing directory, to PREFIX/samtools.mmm.mmm.tmp.nnnn.bam, where mmm is unique to this invocation of the sort command.

By default, any temporary files are written alongside the output file, as out.bam.tmp.nnnn.bam, or if output is to standard output, in the current directory as samtools.mmm.mmm.tmp.nnnn.bam.

-@ INT

Set number of sorting and compression threads. By default, operation is single-threaded.

--no-PG

Do not add a @PG line to the header of the output file.

Ordering Rules

The following rules are used for ordering records.

If option -t is in use, records are first sorted by the value of the given alignment tag, and then by position or name (if using -n). For example, “-t RG” will make read group the primary sort key.  The rules for ordering by tag are:

When the -n option is present, records are sorted by name.  Names are compared so as to give a “natural” ordering — i.e. sections consisting of digits are compared numerically while all other sections are compared based on their binary representation.  This means “a1” will come before “b1” and “a9” will come before “a10”. Records with the same name will be ordered according to the values of the READ1 and READ2 flags (see flags).

When the -n option is not present, reads are sorted by reference (according to the order of the @SQ header records), then by position in the reference, and then by the REVERSE flag.

Note

Historically samtools sort also accepted a less flexible way of specifying the final and temporary output filenames:

samtools sort [-f] [-o] in.bam out.prefix

This has now been removed. The previous out.prefix argument (and -f option, if any) should be changed to an appropriate combination of -T PREFIX and -o FILE.  The previous -o option should be removed, as output defaults to standard output.

Author

Written by Heng Li from the Sanger Institute with numerous subsequent modifications.

See Also

samtools(1), samtools-collate(1), samtools-merge(1)

Samtools website: <http://www.htslib.org/>

Referenced By

samtools(1), samtools-ampliconclip(1), samtools-collate(1), samtools-depth(1), samtools-fixmate(1), samtools-markdup(1), samtools-merge(1), samtools-mpileup(1).

7 July 2021 samtools-1.13 Bioinformatics tools