@DocumentedFeature public class SplitSamByLibrary extends CommandLineProgram
This tool takes a SAM or BAM file and separates all the reads into one SAM or BAM file per library name. Reads that do not have a read group specified or whose read group does not have a library name are written to a file called 'unknown.' The format (SAM or BAM) of the output files matches that of the input file.
java -jar picard.jar SplitSamByLibrary \
I=input_reads.bam \
O=/output/directory/
| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT |
|
static int |
NO_LIBRARIES_SPECIFIED_IN_HEADER |
|
File |
OUTPUT |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY| Constructor | Description |
|---|---|
SplitSamByLibrary() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="The SAM or BAM file to be split. ")
public File INPUT
@Argument(shortName="O",
doc="The directory where the library SAM or BAM files should be written (defaults to the current directory). ",
optional=true)
public File OUTPUT
public static final int NO_LIBRARIES_SPECIFIED_IN_HEADER
public static void main(String[] args)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram