Package picard.fingerprint
Class ClusterCrosscheckMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.fingerprint.ClusterCrosscheckMetrics
Summary
Clusters the results from aCrosscheckFingerprints
run according to the LOD score. The resulting metric file
can be used to assist diagnosing results from CrosscheckFingerprints
. It clusters the connectivity graph between the
different groups. Two groups are connected if they have a LOD score greater than the LOD_THRESHOLD
.
Details
The results of runningCrosscheckFingerprints
can be difficult to analyze, especially when many groups are
related (meaning LOD greater than LOD_THRESHOLD
) in non-transitive manner (A is related to B, B is related to C,
but A doesn't seem to be related to C.) ClusterCrosscheckMetrics
clusters the metrics from CrosscheckFingerprints
so that all the groups in a cluster are related to each other either directly, or indirectly (thus A, B and C would
end up in one cluster.) Two samples can only be in two different clusters if all the samples from these two clusters
do not get high LOD scores when compared to each other.
Example
java -jar picard.jar ClusterCrosscheckMetrics \ INPUT=sample.crosscheck_metrics \ LOD_THRESHOLD=3 \ OUTPUT=sample.clustered.crosscheck_metricsThe resulting file, consists of the
ClusteredCrosscheckMetric
class and contains the original crosscheck metric
values, for groups that end-up in the same clusters (regardless of LOD score of each comparison). In addition it notes
the ClusteredCrosscheckMetric.CLUSTER
identifier and the size of the cluster (in ClusteredCrosscheckMetric.CLUSTER_SIZE
.)
Groups that do not have high LOD scores with any other group (including itself!) will not be included in the metric file.
Note that cross-group comparisons are not included in the metric file.-
Field Summary
FieldsFields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
-
Field Details
-
INPUT
-
OUTPUT
@Argument(shortName="O", optional=true, doc="Output file to write metrics to. Will write to stdout if null.") public File OUTPUT -
LOD_THRESHOLD
@Argument(shortName="LOD", doc="LOD score to be used as the threshold for clustering.") public double LOD_THRESHOLD
-
-
Constructor Details
-
ClusterCrosscheckMetrics
public ClusterCrosscheckMetrics()
-
-
Method Details
-
doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
-