public class GenotypeConcordance extends CommandLineProgram
Modifier and Type | Field and Description |
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String |
CALL_SAMPLE |
File |
CALL_VCF |
static String |
CONTINGENCY_METRICS_FILE_EXTENSION |
static String |
DETAILED_METRICS_FILE_EXTENSION |
protected GenotypeConcordanceCounts |
indelCounter |
boolean |
INTERSECT_INTERVALS |
List<File> |
INTERVALS |
int |
MIN_DP |
int |
MIN_GQ |
boolean |
MISSING_SITES_HOM_REF |
File |
OUTPUT |
boolean |
OUTPUT_ALL_ROWS |
protected GenotypeConcordanceCounts |
snpCounter |
static String |
SUMMARY_METRICS_FILE_EXTENSION |
String |
TRUTH_SAMPLE |
File |
TRUTH_VCF |
boolean |
USE_VCF_INDEX |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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GenotypeConcordance() |
Modifier and Type | Method and Description |
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protected String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
|
protected int |
doWork()
Do the work after command line has been parsed.
|
GenotypeConcordanceCounts |
getIndelCounter() |
GenotypeConcordanceCounts |
getSnpCounter() |
static void |
main(String[] args) |
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="O", doc="Basename for the two metrics files that are to be written. Resulting files will be
@Option(shortName="TS", doc="The name of the truth sample within the truth VCF") public String TRUTH_SAMPLE
@Option(shortName="CS", doc="The name of the call sample within the call VCF") public String CALL_SAMPLE
@Option(doc="One or more interval list files that will be used to limit the genotype concordance. Note - if intervals are specified, the VCF files must be indexed.") public List<File> INTERVALS
@Option(doc="If true, multiple interval lists will be intersected. If false multiple lists will be unioned.") public boolean INTERSECT_INTERVALS
@Option(doc="Genotypes below this genotype quality will have genotypes classified as LowGq.") public int MIN_GQ
@Option(doc="Genotypes below this depth will have genotypes classified as LowDp.") public int MIN_DP
@Option(doc="If true, output all rows in detailed statistics even when count == 0. When false only output rows with non-zero counts.") public boolean OUTPUT_ALL_ROWS
@Option(doc="If true, use the VCF index, else iterate over the entire VCF.", optional=true) public boolean USE_VCF_INDEX
@Option(shortName="MISSING_HOM", doc="Default is false, which follows the GA4GH Scheme. If true, missing sites in the truth set will be treated as HOM_REF sites and sites missing in both the truth and call sets will be true negatives. Useful when hom ref sites are left out of the truth set. This flag can only be used with a high confidence interval list.") public boolean MISSING_SITES_HOM_REF
public static final String SUMMARY_METRICS_FILE_EXTENSION
public static final String DETAILED_METRICS_FILE_EXTENSION
public static final String CONTINGENCY_METRICS_FILE_EXTENSION
protected GenotypeConcordanceCounts snpCounter
protected GenotypeConcordanceCounts indelCounter
public GenotypeConcordanceCounts getSnpCounter()
public GenotypeConcordanceCounts getIndelCounter()
public static void main(String[] args)
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram