1. Command line to start Picard has changed. Use:
    • java -jar picard.jar <tool> <parameters>
    instead of:
    • java -jar <tool>.jar <parameters>
  1. To skip writing files for unmapped reads (FASTQ when using IlluminaBasecallsToFastq or SAM/BAM when using IlluminaBasecallsToSam), leave out the line with 'N' mapping in the multiplex parameters file.
  1. GZIP compression level can now be set with COMPRESSION_LEVEL command line parameter. Accepted values are 1-9.
Last modified 7 years ago Last modified on Jan 20, 2015, 8:25:57 AM