@DocumentedFeature public class CollectVariantCallingMetrics extends CommandLineProgram
| Modifier and Type | Class | Description |
|---|---|---|
static class |
CollectVariantCallingMetrics.VariantCallingDetailMetrics |
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
|
static class |
CollectVariantCallingMetrics.VariantCallingSummaryMetrics |
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
|
| Modifier and Type | Field | Description |
|---|---|---|
File |
DBSNP |
|
boolean |
GVCF_INPUT |
|
File |
INPUT |
|
File |
OUTPUT |
|
File |
SEQUENCE_DICTIONARY |
|
File |
TARGET_INTERVALS |
|
int |
THREAD_COUNT |
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 |
|---|---|
CollectVariantCallingMetrics() |
| 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="Input vcf file for analysis")
public File INPUT
@Argument(shortName="O",
doc="Path (except for the file extension) of output metrics files to write.")
public File OUTPUT
@Argument(doc="Reference dbSNP file in dbSNP or VCF format.") public File DBSNP
@Argument(shortName="TI",
doc="Target intervals to restrict analysis to.",
optional=true)
public File TARGET_INTERVALS
@Argument(shortName="SD",
optional=true,
doc="If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.")
public File SEQUENCE_DICTIONARY
@Argument(doc="Set to true if running on a single-sample gvcf.",
optional=true)
public boolean GVCF_INPUT
@Argument public int THREAD_COUNT
public static void main(String[] args)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgram