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

Picard modifications

We have made some changes to 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 for Picard can be found at


Binary releases of the modified Picard.

Fork version Date Binary Picard version
1.128-5 October 14, 2015 1.128
1.128-4 March 6, 2015 1.128
1.128-3 January 20, 2015 1.128 Notes
1.120-2 September 26, 2014 1.120
1.115-1 August 19, 2014 1.115

Documentation of changes

Fork release version 5

  1. [Picard AddOrReplaceReadGroups]: Add Read Group Library tag to SAM records

Fork release version 4

  1. [Picard IlluminaBasecallsToFastq and IlluminaBasecallsToSam]: Allow barcode files with 0 length

Fork release version 3

  1. [Picard - IlluminaBasecallsToFastq and IlluminaBasecallsToSam]: Do not write FASTQ/BAM/SAM files for unmapped barcode if no 'N' in mapping file
  2. [HTSJDK]: Add support for setting compression level when opening GZIP files for writing
  3. [Picard]: Set compression level to value of COMPRESSION_LEVEL command line parameter

Fork release version 2

  1. [Picard - CheckIlluminaDirectory]: Use TileMetrics.bin instead of TileMetricsOut.bin if it is larger
  2. [Picard - CheckIlluminaDirectory]: Log failures with ERROR level instead of INFO level

Fork release version 1

  1. [HTSJDK]: Print regular log messages to stdout and error messages to stderr
  2. [Picard]: Use nnordborg/htsjdk/lorry branch instead of samtools/htsjdk/master
  3. [Picard]: Print information messages to stdout instead of stderr
  4. [Picard - ExtractIlluminaBarcodes]: Added support for FIRST_TILE and TILE_LIMIT parameters
  5. [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

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