java -jar picard.jar ClusterCrosscheckMetrics \
INPUT=sample.crosscheck_metrics \
LOD_THRESHOLD=3 \
OUTPUT=sample.clustered.crosscheck_metrics
The resulting file, consists of the {@link 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 {@link ClusteredCrosscheckMetric#CLUSTER} identifier and the size of the cluster (in {@link 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.
java -jar picard.jar ClusterCrosscheckMetrics \
INPUT=sample.crosscheck_metrics \
LOD_THRESHOLD=3 \
OUTPUT=sample.clustered.crosscheck_metrics
The 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.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Required Arguments | |||
| --INPUT -I |
null | The cross-check metrics file to be clustered. | |
| Optional Tool Arguments | |||
| --arguments_file |
[] | read one or more arguments files and add them to the command line | |
| --help -h |
false | display the help message | |
| --LOD_THRESHOLD -LOD |
0.0 | LOD score to be used as the threshold for clustering. | |
| --OUTPUT -O |
null | Output file to write metrics to. Will write to stdout if null. | |
| --version |
false | display the version number for this tool | |
| Optional Common Arguments | |||
| --COMPRESSION_LEVEL |
5 | Compression level for all compressed files created (e.g. BAM and VCF). | |
| --CREATE_INDEX |
false | Whether to create a BAM index when writing a coordinate-sorted BAM file. | |
| --CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
| --GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
| --MAX_RECORDS_IN_RAM |
500000 | When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed. | |
| --QUIET |
false | Whether to suppress job-summary info on System.err. | |
| --REFERENCE_SEQUENCE -R |
null | Reference sequence file. | |
| --TMP_DIR |
[] | One or more directories with space available to be used by this program for temporary storage of working files | |
| --USE_JDK_DEFLATER -use_jdk_deflater |
false | Use the JDK Deflater instead of the Intel Deflater for writing compressed output | |
| --USE_JDK_INFLATER -use_jdk_inflater |
false | Use the JDK Inflater instead of the Intel Inflater for reading compressed input | |
| --VALIDATION_STRINGENCY |
STRICT | Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. | |
| --VERBOSITY |
INFO | Control verbosity of logging. | |
| Advanced Arguments | |||
| --showHidden |
false | display hidden arguments | |
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
read one or more arguments files and add them to the command line
List[File] []
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
Google Genomics API client_secrets.json file path.
String client_secrets.json
display the help message
boolean false
The cross-check metrics file to be clustered.
R File null
LOD score to be used as the threshold for clustering.
double 0.0 [ [ -∞ ∞ ] ]
When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
Integer 500000 [ [ -∞ ∞ ] ]
Output file to write metrics to. Will write to stdout if null.
File null
Whether to suppress job-summary info on System.err.
Boolean false
Reference sequence file.
File null
display hidden arguments
boolean false
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:
ValidationStringency STRICT
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.0.11.0 built at 23-11-2018 02:11:49.