Sorts a SAM or BAM file in a specified order, indexes BAM files, and interconverts SAM and BAM files.
Author: Picard team (SAMTools), Marc-Danie Nazaire (Broad Institute)
Contact:
Algorithm Version: 4
The Picard.SortSam module sorts SAM or BAM files, indexes BAM files, and interconverts SAM and BAM files. The module implements the SortSam function from Picard (Github).
BAM format is the binary equivalent of the Sequence Alignment Map (SAM) format and a BAM file can be up to four times smaller than its SAM equivalent. For detailed information on these formats, see the September 2014 article titled Sequence Alignment/Map Format Specification by the SAM/BAM Format Specification Working Group.
Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]
Name | Description |
---|---|
input file * | Input file in SAM or BAM format |
sort order * |
Specifies the sort order by the following options:
Default: coordinate |
output format * | Whether the file output format should be SAM or BAM. Default: BAM |
output prefix * | The prefix to use for the output file name. |
* - required
BAM or SAM format file
This is the sorted SAM or BAM file.
This file contains the index for the coordinate sorted BAM output file.
Task Type:
Preprocess & Utilities
CPU Type:
any
Operating System:
any
Language:
Java (minimum version 1.6)
Version | Release Date | Description |
---|---|---|
4 | 2013-05-07 | Renamed from SortSam to Picard.SortSam |
3 | 2011-04-01 | Added output format parameter |
2 | 2011-02-28 | Added 1 sec to index file timestamp, and added notes to doc |
1 | 2011-02-15 | |
2014-09-26 |