Tally the counts of UMIs in duplicate sets within a bam.
This tool collects the Histogram of the number of duplicate sets that contain a given number of UMIs. Understanding this distribution can help understand the role that the UMIs have in the determination of consensus sets, the risk of UMI collisions, and of spurious reads that result from uncorrected UMIs.
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 |
Input (indexed) BAM/CRAM file. | ||
| --OUTPUT -O |
Write metrics to this file | ||
| Optional Tool Arguments | |||
| --arguments_file |
read one or more arguments files and add them to the command line | ||
| --BARCODE_BQ |
BQ | Barcode Quality SAM tag. | |
| --BARCODE_TAG |
RX | Barcode SAM tag. | |
| --FILTER_UNPAIRED_READS -FUR |
true | Whether to filter unpaired reads from the input. | |
| --help -h |
false | display the help message | |
| --MINIMUM_BARCODE_BQ -BQ |
30 | minimal value for the base quality of all the bases in a molecular barcode, for it to be used. | |
| --MINIMUM_MQ -MQ |
30 | minimal value for the mapping quality of the reads to be used in the estimation. | |
| --PROGRESS_STEP_INTERVAL |
1000000 | The interval between which progress will be displayed. | |
| --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 an index when writing VCF or coordinate sorted BAM output. | |
| --CREATE_MD5_FILE |
false | Whether to create an MD5 digest for any BAM or FASTQ files created. | |
| --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 |
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] []
Barcode Quality SAM tag.
String BQ
Barcode SAM tag.
String RX
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
Whether to filter unpaired reads from the input.
boolean true
display the help message
boolean false
Input (indexed) BAM/CRAM file.
R PicardHtsPath null
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 [ [ -∞ ∞ ] ]
minimal value for the base quality of all the bases in a molecular barcode, for it to be used.
Integer 30 [ [ 0 255 ] ]
minimal value for the mapping quality of the reads to be used in the estimation.
Integer 30 [ [ 0 255 ] ]
Write metrics to this file
R File null
The interval between which progress will be displayed.
int 1000000 [ [ -∞ ∞ ] ]
Whether to suppress job-summary info on System.err.
Boolean false
Reference sequence file.
PicardHtsPath 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 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.