NOTE!! |
The modifications listed here are obsolete. Most things have already been fixed in a newer Picard version (2.20 when writing this) or can be worked around in ways that are better than using a modified version. For more information see http://baseplugins.thep.lu.se/ticket/1160 |
Picard modifications
We have made some changes to Picard, http://broadinstitute.github.io/picard/, that we feel are useful for a wider audience. The changes can be found and tracked on a GitHub fork of the main Picard and HTSJDK projects:
Documentation
Documentation for Picard can be found at http://broadinstitute.github.io/picard/
Downloads
Binary releases of the modified Picard.
Fork version | Date | Binary | Picard version | |
1.128-5 | October 14, 2015 | picard-tools-1.128-5.zip | 1.128 | |
1.128-4 | March 6, 2015 | picard-tools-1.128-4.zip | 1.128 | |
1.128-3 | January 20, 2015 | picard-tools-1.128-3.zip | 1.128 | Notes |
1.120-2 | September 26, 2014 | picard-tools-1.120-2.zip | 1.120 | |
1.115-1 | August 19, 2014 | picard-tools-1.115-1.zip | 1.115 |
Documentation of changes
Fork release version 5
- [Picard AddOrReplaceReadGroups]: Add Read Group Library tag to SAM records
Fork release version 4
- [Picard IlluminaBasecallsToFastq and IlluminaBasecallsToSam]: Allow barcode files with 0 length
Fork release version 3
- [Picard - IlluminaBasecallsToFastq and IlluminaBasecallsToSam]: Do not write FASTQ/BAM/SAM files for unmapped barcode if no 'N' in mapping file
- [HTSJDK]: Add support for setting compression level when opening GZIP files for writing
- [Picard]: Set compression level to value of COMPRESSION_LEVEL command line parameter
Fork release version 2
- [Picard - CheckIlluminaDirectory]: Use TileMetrics.bin instead of TileMetricsOut.bin if it is larger
- [Picard - CheckIlluminaDirectory]: Log failures with ERROR level instead of INFO level
Fork release version 1
- [HTSJDK]: Print regular log messages to stdout and error messages to stderr
- [Picard]: Use nnordborg/htsjdk/lorry branch instead of samtools/htsjdk/master
- [Picard]: Print information messages to stdout instead of stderr
- [Picard - ExtractIlluminaBarcodes]: Added support for FIRST_TILE and TILE_LIMIT parameters
- [Picard - IlluminaBaseCallsToFastq]: Closing 'underlyingIterator' when the 'CountLimitedIterator' is closed (to get rid of the 'Too many open files' problem)
Last modified 21 months ago
Last modified on Jun 28, 2019, 10:59:18 AM
Attachments (5)
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picard-tools-1.115-1.zip (48.1 MB) - added by 7 years ago.
Picard 1.115-1
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picard-tools-1.120-2.zip (49.9 MB) - added by 6 years ago.
Picard 1.120-2
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picard-tools-1.128-3.zip (7.7 MB) - added by 6 years ago.
Picard 1.128-3
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picard-tools-1.128-4.zip (7.7 MB) - added by 6 years ago.
Picard 1.128-4
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picard-tools-1.128-5.zip (7.7 MB) - added by 5 years ago.
Picard 1.128-5