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 \Please see the metrics definitions page on TargetedPcrMetrics for detailed explanations of the output metrics produced by this tool.
I=input.bam \
O=output_pcr_metrics.txt \
R=reference.fasta \
AMPLICON_INTERVALS=amplicon.interval_list \
TARGET_INTERVALS=targets.interval_list
Category Diagnostics and Quality Control
Overview
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 \\Please see the metrics definitions page on TargetedPcrMetrics for detailed explanations of the output metrics produced by this tool.
I=input.bam \\
O=output_pcr_metrics.txt \\
R=reference.fasta \\
AMPLICON_INTERVALS=amplicon.interval_list \\
TARGET_INTERVALS=targets.interval_list
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 |
null | An interval list file that contains the locations of the baits used. | |
--INPUT -I |
null | An aligned SAM or BAM file. | |
--OUTPUT -O |
null | 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 |
null | 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 |
null | 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 |
null | 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 |
null | 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 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.
--ALLELE_FRACTION / NA
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 / NA
read one or more arguments files and add them to the command line
List[File] []
--CLIP_OVERLAPPING_READS / NA
True if we are to clip overlapping reads, false otherwise.
boolean false
--COMPRESSION_LEVEL / NA
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 / NA
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
--CREATE_MD5_FILE / NA
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 / NA
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--INCLUDE_INDELS / NA
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 / 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 [ [ -∞ ∞ ] ]
--METRIC_ACCUMULATION_LEVEL / -LEVEL
The level(s) at which to accumulate metrics.
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 / NA
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 / NA
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 / NA
An optional file to output per target coverage information to.
File null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--SAMPLE_SIZE / NA
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 / NA
Output for Theoretical Sensitivity metrics where the allele fractions are provided by the ALLELE_FRACTION argument.
File null
--TMP_DIR / NA
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 / 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
--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
--version / NA
display the version number for this tool
boolean false
GATK version 4.1.3.0 built at Sat, 23 Nov 2019 16:20:54 -0500.
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