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, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor | Description |
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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, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="O", doc="Path (except for the file extension) of output metrics files to write.") public File OUTPUT
@Option(shortName="TI", doc="Target intervals to restrict analysis to.", optional=true) public File TARGET_INTERVALS
@Option(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
@Option(doc="Set to true if running on a single-sample gvcf.", optional=true) public boolean GVCF_INPUT
@Option public int THREAD_COUNT
public static void main(String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram