SetNmAndUqTags@DocumentedFeature public class SetNmMdAndUqTags extends CommandLineProgram
This tool takes in a coordinate-sorted SAM or BAM file and calculates the NM, MD, and UQ tags by comparing with the reference.
This may be needed when MergeBamAlignment was run with SORT_ORDER other than 'coordinate' and thus could not fix these tags then. The input must be coordinate sorted in order to run. If specified, the MD and NM tags can be ignored and only the UQ tag be set.
A BAM or SAM output file with recalculated NM, MD, and UQ tags
java -jar picard.jar SetNmMdAndUqTags \
R=reference_sequence.fasta \
I=sorted.bam \
O=fixed.bam
| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT |
|
boolean |
IS_BISULFITE_SEQUENCE |
|
File |
OUTPUT |
|
boolean |
SET_ONLY_UQ |
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 |
|---|---|
SetNmMdAndUqTags() |
| Modifier and Type | Method | Description |
|---|---|---|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] argv) |
|
protected boolean |
requiresReference() |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser@Argument(doc="The BAM or SAM file to fix. ",
shortName="I")
public File INPUT
@Argument(doc="The fixed BAM or SAM output file. ",
shortName="O")
public File OUTPUT
@Argument(doc="Whether the file contains bisulfite sequence (used when calculating the NM tag).") public boolean IS_BISULFITE_SEQUENCE
@Argument(doc="Only set the UQ tag, ignore MD and NM.") public boolean SET_ONLY_UQ
protected boolean requiresReference()
requiresReference in class CommandLineProgrampublic static void main(String[] argv)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram