samtools-collate - shuffles and groups reads together by their names
samtools collate [
options]
in.sam|
in.bam|
in.cram
[
<prefix>]
Shuffles and groups reads together by their names. A faster alternative to a
full query name sort,
collate ensures that reads of the same name are
grouped together in contiguous groups, but doesn't make any guarantees about
the order of read names between groups.
The output from this command should be suitable for any operation that requires
all reads from the same template to be grouped together.
If present, <prefix> is used to name the temporary files that collate uses
when sorting the data. If neither the
-O nor
-o options are
used, <prefix> must be present and collate will use it to make an output
file name by appending a suffix depending on the format written (.bam by
default).
If either the
-O or
-o option is used, <prefix> is optional.
If <prefix> is absent, collate will write the temporary files to a
system-dependent location (/tmp on UNIX).
Using
-f for fast mode will output
only primary alignments that
have either the READ1
or READ2 flags set (but not both). Any other
alignment records will be filtered out. The collation will only work correctly
if there are no more than two reads for any given QNAME after filtering.
Fast mode keeps a buffer of alignments in memory so that it can write out most
pairs as soon as they are found instead of storing them in temporary files.
This allows collate to avoid some work and so finish more quickly compared to
the standard mode. The number of alignments held can be changed using
-r, storing more alignments uses more memory but increases the number
of pairs that can be written early.
While collate normally randomises the ordering of read pairs, fast mode does
not. Position-dependent biases that would normally be broken up can remain in
the fast collate output. It is therefore not a good idea to use fast mode when
preparing data for programs that expect randomly ordered paired reads. For
example using fast collate instead of the standard mode may lead to
significantly different results from aligners that estimate library insert
sizes on batches of reads.
- -O
- Output to stdout. This option cannot be used with
'-o'.
- -o FILE
- Write output to FILE. This option cannot be used with
'-O'.
- -u
- Write uncompressed BAM output
-
-l INT
- Compression level. [1]
-
-n INT
- Number of temporary files to use. [64]
- -f
- Fast mode (primary alignments only).
-
-r INT
- Number of reads to store in memory (for use with -f).
[10000]
- --no-PG
- Do not add a @PG line to the header of the output
file.
-
-@, --threads INT
- Number of input/output compression threads to use in
addition to main thread [0].
Written by Heng Li from the Sanger Institute and extended by Andrew Whitwham.
samtools(1),
samtools-sort(1)
Samtools website: <
http://www.htslib.org/>