Overview of Illumina2bam Picard command-line tools

Illumina2bam is a collection of tools to generate or process BAM/SAM files using Picard Java API.

It currently includes Illumina2bam, BamIndexDecoder, BamReadTrimmer, BamMerger, BamTagStripper, BamQualityQuantisation, ChangeBamHeader, SplitBamByReadGroup and AlignmentFilter etc.

The Picard command-line tools are packaged as executable jar files. They require Java 1.6. They can be invoked as follows:

java jvm-args -jar PicardCommand.jar OPTION1=value1 OPTION2=value2...

Most of the commands are designed to run in 2GB of JVM, so the JVM argument -Xmx2g is recommended.

Standard Options

The following options are relevant for most Picard programs: