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.
Output to stdout. This option cannot be used with '-o'.
- -o FILE
Write output to FILE. This option cannot be used with '-O'.
Write uncompressed BAM output
- -l INT
Compression level. 
- -n INT
Number of temporary files to use. 
Fast mode (primary alignments only).
- -r INT
Number of reads to store in memory (for use with -f). 
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 .
Written by Heng Li from the Sanger Institute and extended by Andrew Whitwham.
Samtools website: <http://www.htslib.org/>
samtools(1), samtools-fixmate(1), samtools-markdup(1), samtools-sort(1).