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.

Category Diagnostics and Quality Control

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Overview

A CLP that, tallies the number of UMIs in a duplicate set across the entire bam and produces a histogram. @author Yossi Farjoun

CollectUmiPrevalenceMetrics (Picard) specific arguments

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

Argument details

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.

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--arguments_file

read one or more arguments files and add them to the command line

List[File]  []

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--BARCODE_BQ

Barcode Quality SAM tag.

String  BQ

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--BARCODE_TAG

Barcode SAM tag.

String  RX

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--COMPRESSION_LEVEL

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]

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--CREATE_INDEX

Whether to create an index when writing VCF or coordinate sorted BAM output.

Boolean  false

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--CREATE_MD5_FILE

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false

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--FILTER_UNPAIRED_READS / -FUR

Whether to filter unpaired reads from the input.

boolean  true

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--help / -h

display the help message

boolean  false

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--INPUT / -I

Input (indexed) BAM/CRAM file.

R PicardHtsPath  null

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--MAX_RECORDS_IN_RAM

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  [ [ -∞  ∞ ] ]

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--MINIMUM_BARCODE_BQ / -BQ

minimal value for the base quality of all the bases in a molecular barcode, for it to be used.

Integer  30  [ [ 0  255 ] ]

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--MINIMUM_MQ / -MQ

minimal value for the mapping quality of the reads to be used in the estimation.

Integer  30  [ [ 0  255 ] ]

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--OUTPUT / -O

Write metrics to this file

R File  null

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--PROGRESS_STEP_INTERVAL

The interval between which progress will be displayed.

int  1000000  [ [ -∞  ∞ ] ]

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--QUIET

Whether to suppress job-summary info on System.err.

Boolean  false

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--REFERENCE_SEQUENCE / -R

Reference sequence file.

PicardHtsPath  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--TMP_DIR

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []

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--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false

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--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false

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--VALIDATION_STRINGENCY

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:

STRICT

LENIENT

SILENT

ValidationStringency  STRICT

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--VERBOSITY

Control verbosity of logging.

The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR

WARNING

INFO

DEBUG

LogLevel  INFO

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--version

display the version number for this tool

boolean  false

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 15:34:15 -0400.