Estimates the rate of independent replication rate of reads within a bam.

This tool estimates the fraction of the input reads which would be marked as duplicates but are actually biological replicates, independent observations of the data.

The tools examines duplicate sets of size 2 and 3 that overlap known heterozygous sites of the sample. The tool classifies these duplicate sets into heterogeneous and homogeneous sets (those that contain the two alleles that are present in the variant and those that only contain one of them). From this the toolestimates the fraction of duplicates that arose from different original molecules, i.e. independently.

Usage example:

java -jar picard.jar CollectIndependentReplicateMetrics \
    I=input.bam \
    V=input.vcf \
    O=output.independent_replicates_metrics \

Category Diagnostics and Quality Control

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Overview

A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam. That is, it estimates the fraction of the reads which look like duplicates (in the MarkDuplicates sense of the word) but are actually independent observations of the data. In the presence of Unique Molecular Identifiers (UMIs), various metrics are collected regarding the utility of the UMI's for the purpose of increasing coverage.

The estimation is based on duplicate-sets of size 2 and 3 and gives separate estimates from each. The assumption is that the duplication rate (biological or otherwise) is independent of the duplicate-set size. A significant difference between the two rates may be an indication that this assumption is incorrect.

The duplicate sets are found using the mate-cigar tag (MC) which is added by picard.sam.MergeBamAlignment , or picard.sam.FixMateInformation. This program will not work without the MC tag.

Explanation of the calculation behind the estimation can be found in the IndependentReplicateMetric class.

The calculation Assumes a diploid organism (more accurately, assumes that only two alleles can appear at a HET site and that these two alleles will appear at equal probabilities. It requires as input a VCF with genotypes for the sample in question. NOTE: This class is very much in alpha stage, and still under heavy development (feel free to join!)

CollectIndependentReplicateMetrics (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	null	Input (indexed) BAM file.
--OUTPUT  -O	null	Write metrics to this file
--VCF  -V	null	Input VCF file
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--BARCODE_BQ	QX	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
--MATRIX_OUTPUT  -MO	null	Write the confusion matrix (of UMIs) to this file
--MINIMUM_BARCODE_BQ  -MBQ	30	minimal value for the base quality of all the bases in a molecular barcode, for it to be used.
--MINIMUM_BQ  -BQ	17	minimal value for the base quality of a base to be used in the estimation.
--MINIMUM_GQ  -GQ	90	minimal value for the GQ field in the VCF to use variant site.
--MINIMUM_MQ  -MQ	40	minimal value for the mapping quality of the reads to be used in the estimation.
--PROGRESS_STEP_INTERVAL	100000	The interval between which progress will be displayed.
--SAMPLE  -ALIAS	null	Name of sample to look at in VCF. Can be omitted if VCF contains only one sample.
--STOP_AFTER	0	Number of sets to examine before stopping.
--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

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 / NA

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

List[File]  []

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--BARCODE_BQ / NA

Barcode Quality SAM tag.

String  QX

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--BARCODE_TAG / NA

Barcode SAM tag.

String  RX

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--COMPRESSION_LEVEL / NA

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

int  5  [ [ -∞  ∞ ] ]

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--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false

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--CREATE_MD5_FILE / NA

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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--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json

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--help / -h

display the help message

boolean  false

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--INPUT / -I

Input (indexed) BAM file.

R File  null

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--MATRIX_OUTPUT / -MO

Write the confusion matrix (of UMIs) to this file

File  null

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--MAX_RECORDS_IN_RAM / NA

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 / -MBQ

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

Integer  30  [ [ -∞  ∞ ] ]

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--MINIMUM_BQ / -BQ

minimal value for the base quality of a base to be used in the estimation.

Integer  17  [ [ -∞  ∞ ] ]

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--MINIMUM_GQ / -GQ

minimal value for the GQ field in the VCF to use variant site.

Integer  90  [ [ -∞  ∞ ] ]

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--MINIMUM_MQ / -MQ

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

Integer  40  [ [ -∞  ∞ ] ]

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--OUTPUT / -O

Write metrics to this file

R File  null

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--PROGRESS_STEP_INTERVAL / NA

The interval between which progress will be displayed.

int  100000  [ [ -∞  ∞ ] ]

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--QUIET / NA

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

Boolean  false

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--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null

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--SAMPLE / -ALIAS

Name of sample to look at in VCF. Can be omitted if VCF contains only one sample.

String  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--STOP_AFTER / NA

Number of sets to examine before stopping.

Integer  0  [ [ -∞  ∞ ] ]

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--TMP_DIR / NA

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 / NA

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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--VCF / -V

Input VCF file

R File  null

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--VERBOSITY / NA

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 / NA

display the version number for this tool

boolean  false

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GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.