Uses of Class
uk.ac.sanger.npg.picard.PicardCommandLine

Packages that use PicardCommandLine

uk.ac.sanger.npg.illumina
uk.ac.sanger.npg.picard

Uses of PicardCommandLine in uk.ac.sanger.npg.illumina

Subclasses of PicardCommandLine in uk.ac.sanger.npg.illumina

class

Illumina2bam This is the main class to convert Illumina BCL files to BAM

Uses of PicardCommandLine in uk.ac.sanger.npg.picard

Subclasses of PicardCommandLine in uk.ac.sanger.npg.picard

class	AlignmentFilter
class	BamIndexDecoder This class is used decode the multiplexed bam file.
class	BamMerger A command-line tool to merge BAM/SAM alignment info in a bam with the data in an unmapped BAM file, producing a third BAM file that has alignment data and all the additional data from the unmapped BAM.
class	BamQualityQuantisation
class	BamReadTrimmer The class to strip part of a read (fixed position) - typically a prefix of the forward read, and optionally place this and its quality in BAM tags.
class	BamTagStripper
class	ChangeBamHeader
class	SplitBamByReadGroup