samtools-sort - sorts SAM/BAM/CRAM files
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]
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.
- -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.
- --template-coordinate
- Sorts by template-coordinate, whereby the sort order (@HD SO) is
unsorted, the group order (GO) is query, and the sub-sort
(SS) is template-coordinate.
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:
- Records that do not have the tag are sorted before ones that do.
- If the types of the tags are different, they will be sorted so that single
character tags (type A) come before array tags (type B), then string tags
(types H and Z), then numeric tags (types f and i).
- Numeric tags (types f and i) are compared by value. Note that comparisons
of floating-point values are subject to issues of rounding and
precision.
- String tags (types H and Z) are compared based on the binary contents of
the tag using the C strcmp(3) function.
- Character tags (type A) are compared by binary character value.
- No attempt is made to compare tags of other types — notably type B
array values will not be compared.
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 --template-coordinate option is in use, the reads
are sorted by:
- 1.
- The earlier unclipped 5' coordinate of the template.
- 2.
- The higher unclipped 5' coordinate of the template.
- 3.
- The library (from the read group).
- 4.
- The molecular identifier (MI tag if present).
- 5.
- The read name.
- 6.
- If unpaired, or if R1 has the lower coordinates of the pair.
When none of the above options are in use, 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.
Written by Heng Li from the Sanger Institute with numerous
subsequent modifications.