CollectTargetedPcrMetrics (Picard) – GATK

Calculate PCR-related metrics from targeted sequencing data.

This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data. It is appropriate for data produced with multiple small-target technologies including exome sequencing an custom amplicon panels such as the Illumina TruSeq Custom Amplicon (TSCA) kit.

If a reference sequence is provided, AT/GC dropout metrics will be calculated and the PER_TARGET_COVERAGE option can be used to output GC content and mean coverage information for each target. The AT/GC dropout metrics indicate the degree of inadequate coverage of a particular region based on its AT or GC content. The PER_TARGET_COVERAGE option can be used to output GC content and mean sequence depth information for every target interval.

Note: Metrics labeled as percentages are actually expressed as fractions!

Usage Example

java -jar picard.jar CollectTargetedPcrMetrics \
       I=input.bam \
       O=output_pcr_metrics.txt \
       R=reference.fasta \
       AMPLICON_INTERVALS=amplicon.interval_list \
       TARGET_INTERVALS=targets.interval_list

Please see the metrics definitions page on TargetedPcrMetrics for detailed explanations of the output metrics produced by this tool.

Category Diagnostics and Quality Control

Overview

Note: Metrics labeled as percentages are actually expressed as fractions!

Usage Example

 java -jar picard.jar CollectTargetedPcrMetrics \\

      I=input.bam \\

      O=output_pcr_metrics.txt \\

      R=reference.fasta \\

      AMPLICON_INTERVALS=amplicon.interval_list \\

      TARGET_INTERVALS=targets.interval_list

Please see the metrics definitions page on TargetedPcrMetrics for detailed explanations of the output metrics produced by this tool.

Collect metric information for target pcr metrics runs. See CollectTargetedMetrics and TargetedPcrMetricsCollector for more information

CollectTargetedPcrMetrics (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
--AMPLICON_INTERVALS -AI		An interval list file that contains the locations of the baits used.
--INPUT -I		An aligned SAM or BAM file.
--OUTPUT -O		The output file to write the metrics to.
--TARGET_INTERVALS -TI		An interval list file that contains the locations of the targets.
Optional Tool Arguments
--ALLELE_FRACTION	[0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5]	Allele fraction for which to calculate theoretical sensitivity.
--arguments_file		read one or more arguments files and add them to the command line
--CLIP_OVERLAPPING_READS	false	True if we are to clip overlapping reads, false otherwise.
--COVERAGE_CAP -covMax	200	Parameter to set a max coverage limit for Theoretical Sensitivity calculations. Default is 200.
--CUSTOM_AMPLICON_SET_NAME -N		Custom amplicon set name. If not provided it is inferred from the filename of the AMPLICON_INTERVALS intervals.
--help -h	false	display the help message
--INCLUDE_INDELS	false	If true count inserted bases as on target and deleted bases as covered by a read.
--METRIC_ACCUMULATION_LEVEL -LEVEL	[ALL_READS]	The level(s) at which to accumulate metrics.
--MINIMUM_BASE_QUALITY -Q	0	Minimum base quality for a base to contribute coverage.
--MINIMUM_MAPPING_QUALITY -MQ	1	Minimum mapping quality for a read to contribute coverage.
--NEAR_DISTANCE	250	The maximum distance between a read and the nearest probe/bait/amplicon for the read to be considered 'near probe' and included in percent selected.
--PER_BASE_COVERAGE		An optional file to output per base coverage information to. The per-base file contains one line per target base and can grow very large. It is not recommended for use with large target sets.
--PER_TARGET_COVERAGE		An optional file to output per target coverage information to.
--SAMPLE_SIZE	10000	Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.
--THEORETICAL_SENSITIVITY_OUTPUT		Output for Theoretical Sensitivity metrics where the allele fractions are provided by the ALLELE_FRACTION argument.
--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.
--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		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.

--ALLELE_FRACTION

Allele fraction for which to calculate theoretical sensitivity.

List[Double] [0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5]

--AMPLICON_INTERVALS / -AI

An interval list file that contains the locations of the baits used.

R File null

--arguments_file

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

List[File] []

--CLIP_OVERLAPPING_READS

True if we are to clip overlapping reads, false otherwise.

boolean false

--COMPRESSION_LEVEL

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

int 5 [ [ -∞ ∞ ] ]

--COVERAGE_CAP / -covMax

Parameter to set a max coverage limit for Theoretical Sensitivity calculations. Default is 200.

int 200 [ [ -∞ ∞ ] ]

--CREATE_INDEX

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

Boolean false

--CREATE_MD5_FILE

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

boolean false

--CUSTOM_AMPLICON_SET_NAME / -N

Custom amplicon set name. If not provided it is inferred from the filename of the AMPLICON_INTERVALS intervals.

String null

--GA4GH_CLIENT_SECRETS

Google Genomics API client_secrets.json file path.

String client_secrets.json

--help / -h

display the help message

boolean false

--INCLUDE_INDELS

If true count inserted bases as on target and deleted bases as covered by a read.

boolean false

--INPUT / -I

An aligned SAM or BAM file.

R File null

--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 [ [ -∞ ∞ ] ]

--METRIC_ACCUMULATION_LEVEL / -LEVEL

The level(s) at which to accumulate metrics.

The --METRIC_ACCUMULATION_LEVEL argument is an enumerated type (Set[MetricAccumulationLevel]), which can have one of the following values:

ALL_READS
SAMPLE
LIBRARY
READ_GROUP

Set[MetricAccumulationLevel] [ALL_READS]

--MINIMUM_BASE_QUALITY / -Q

Minimum base quality for a base to contribute coverage.

int 0 [ [ -∞ ∞ ] ]

--MINIMUM_MAPPING_QUALITY / -MQ

Minimum mapping quality for a read to contribute coverage.

int 1 [ [ -∞ ∞ ] ]

--NEAR_DISTANCE

The maximum distance between a read and the nearest probe/bait/amplicon for the read to be considered 'near probe' and included in percent selected.

int 250 [ [ -∞ ∞ ] ]

--OUTPUT / -O

The output file to write the metrics to.

R File null

--PER_BASE_COVERAGE

An optional file to output per base coverage information to. The per-base file contains one line per target base and can grow very large. It is not recommended for use with large target sets.

File null

--PER_TARGET_COVERAGE

An optional file to output per target coverage information to.

File null

--QUIET

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

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File null

--SAMPLE_SIZE

Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.

int 10000 [ [ -∞ ∞ ] ]

--showHidden / -showHidden

display hidden arguments

boolean false

--TARGET_INTERVALS / -TI

An interval list file that contains the locations of the targets.

R List[File] []

--THEORETICAL_SENSITIVITY_OUTPUT

Output for Theoretical Sensitivity metrics where the allele fractions are provided by the ALLELE_FRACTION argument.

File null

--TMP_DIR

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

List[File] []

--USE_JDK_DEFLATER / -use_jdk_deflater

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

Boolean false

--USE_JDK_INFLATER / -use_jdk_inflater

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

Boolean false

--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

--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

--version

display the version number for this tool

boolean false

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GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.

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Articles in this section

Usage Example

Category Diagnostics and Quality Control

Overview

Usage Example

CollectTargetedPcrMetrics (Picard) specific arguments

Argument details

--AMPLICON_INTERVALS / -AI

--COVERAGE_CAP / -covMax

--CUSTOM_AMPLICON_SET_NAME / -N

--help / -h

--INPUT / -I

--METRIC_ACCUMULATION_LEVEL / -LEVEL

--MINIMUM_BASE_QUALITY / -Q

--MINIMUM_MAPPING_QUALITY / -MQ

--OUTPUT / -O

--REFERENCE_SEQUENCE / -R

--showHidden / -showHidden

--TARGET_INTERVALS / -TI

--USE_JDK_DEFLATER / -use_jdk_deflater

--USE_JDK_INFLATER / -use_jdk_inflater