Collect whole genome sequencing-related metrics. This tool computes metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. These metrics include the percentages of reads that pass minimal base- and mapping- quality filters as well as coverage (read-depth) levels.
The histogram output is optional and for a given run, displays two separate outputs on the y-axis while using a single set of values for the x-axis. Specifically, the first column in the histogram table (x-axis) is labeled 'coverage' and represents different possible coverage depths. However, it also represents the range of values for the base quality scores and thus should probably be labeled 'sequence depth and base quality scores'. The second and third columns (y-axes) correspond to the numbers of bases at a specific sequence depth 'count' and the numbers of bases at a particular base quality score 'baseq_count' respectively.
Although similar to the CollectWgsMetrics tool, the default thresholds for CollectRawWgsMetrics are less stringent. For example, the CollectRawWgsMetrics have base and mapping quality score thresholds set to '3' and '0' respectively, while the CollectWgsMetrics tool has the default threshold values set to '20' (at time of writing). Nevertheless, both tools enable the user to input specific threshold values.
Note: Metrics labeled as percentages are actually expressed as fractions!
Usage example:
java -jar picard.jar CollectRawWgsMetrics \
I=input.bam \
O=output_raw_wgs_metrics.txt \
R=reference.fasta \
INCLUDE_BQ_HISTOGRAM=true
Please see the WgsMetrics documentation for detailed explanations of the output metrics.
Category Diagnostics and Quality Control
Overview
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as CollectWgsMetrics, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap. This tool computes metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. These metrics include the percentages of reads that pass minimal base- and mapping- quality filters as well as coverage (read-depth) levels.The histogram output is optional and for a given run, displays two separate outputs on the y-axis while using a single set of values for the x-axis. Specifically, the first column in the histogram table (x-axis) is labeled 'coverage' and represents different possible coverage depths. However, it also represents the range of values for the base quality scores and thus should probably be labeled 'sequence depth and base quality scores'. The second and third columns (y-axes) correspond to the numbers of bases at a specific sequence depth 'count' and the numbers of bases at a particular base quality score 'baseq_count' respectively.
Although similar to the CollectWgsMetrics tool, the default thresholds for CollectRawWgsMetrics are less stringent. For example, the CollectRawWgsMetrics have base and mapping quality score thresholds set to '3' and '0' respectively, while the CollectWgsMetrics tool has the default threshold values set to '20' (at time of writing). Nevertheless, both tools enable the user to input specific threshold values.
Note: Metrics labeled as percentages are actually expressed as fractions!
Usage example:
java -jar picard.jar CollectRawWgsMetrics \\
I=input.bam \\
O=output_raw_wgs_metrics.txt \\
R=reference.fasta \\
INCLUDE_BQ_HISTOGRAM=true
Please see the WgsMetrics documentation for detailed explanations of the output metrics.
CollectRawWgsMetrics (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 SAM or BAM file. | ||
--OUTPUT -O |
Output metrics file. | ||
--REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
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 | ||
--COUNT_UNPAIRED |
false | If true, count unpaired reads, and paired reads with one end unmapped | |
--COVERAGE_CAP -CAP |
100000 | Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED). | |
--help -h |
false | display the help message | |
--INCLUDE_BQ_HISTOGRAM |
false | Determines whether to include the base quality histogram in the metrics file. | |
--INTERVALS |
An interval list file that contains the positions to restrict the assessment. Please note that all bases of reads that overlap these intervals will be considered, even if some of those bases extend beyond the boundaries of the interval. The ideal use case for this argument is to use it to restrict the calculation to a subset of (whole) contigs. | ||
--LOCUS_ACCUMULATION_CAP |
200000 | At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED). Used to keep memory consumption in check, but could create bias if set too low | |
--MINIMUM_BASE_QUALITY -Q |
3 | Minimum base quality for a base to contribute coverage. N bases will be treated as having a base quality of negative infinity and will therefore be excluded from coverage regardless of the value of this parameter. | |
--MINIMUM_MAPPING_QUALITY -MQ |
0 | Minimum mapping quality for a read to contribute coverage. | |
--READ_LENGTH |
150 | Average read length in the file. Default is 150. | |
--SAMPLE_SIZE |
10000 | Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000. | |
--STOP_AFTER |
-1 | For debugging purposes, stop after processing this many genomic bases. | |
--THEORETICAL_SENSITIVITY_OUTPUT |
Output for Theoretical Sensitivity metrics. | ||
--USE_FAST_ALGORITHM |
false | If true, fast algorithm is used. | |
--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. | |
--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]
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--COUNT_UNPAIRED
If true, count unpaired reads, and paired reads with one end unmapped
boolean false
--COVERAGE_CAP / -CAP
Treat positions with coverage exceeding this value as if they had coverage at this value (but calculate the difference for PCT_EXC_CAPPED).
int 100000 [ [ -∞ ∞ ] ]
--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
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--help / -h
display the help message
boolean false
--INCLUDE_BQ_HISTOGRAM
Determines whether to include the base quality histogram in the metrics file.
boolean false
--INPUT / -I
Input SAM or BAM file.
R File null
--INTERVALS
An interval list file that contains the positions to restrict the assessment. Please note that all bases of reads that overlap these intervals will be considered, even if some of those bases extend beyond the boundaries of the interval. The ideal use case for this argument is to use it to restrict the calculation to a subset of (whole) contigs.
File null
--LOCUS_ACCUMULATION_CAP
At positions with coverage exceeding this value, completely ignore reads that accumulate beyond this value (so that they will not be considered for PCT_EXC_CAPPED). Used to keep memory consumption in check, but could create bias if set too low
int 200000 [ [ -∞ ∞ ] ]
--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 [ [ -∞ ∞ ] ]
--MINIMUM_BASE_QUALITY / -Q
Minimum base quality for a base to contribute coverage. N bases will be treated as having a base quality of negative infinity and will therefore be excluded from coverage regardless of the value of this parameter.
int 3 [ [ -∞ ∞ ] ]
--MINIMUM_MAPPING_QUALITY / -MQ
Minimum mapping quality for a read to contribute coverage.
int 0 [ [ -∞ ∞ ] ]
--OUTPUT / -O
Output metrics file.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--READ_LENGTH
Average read length in the file. Default is 150.
int 150 [ [ -∞ ∞ ] ]
--REFERENCE_SEQUENCE / -R
Reference sequence file.
R File null
--SAMPLE_SIZE
Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000.
int 10000 [ [ -∞ ∞ ] ]
--showHidden / -showHidden
display hidden arguments
boolean false
--STOP_AFTER
For debugging purposes, stop after processing this many genomic bases.
long -1 [ [ -∞ ∞ ] ]
--THEORETICAL_SENSITIVITY_OUTPUT
Output for Theoretical Sensitivity metrics.
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_FAST_ALGORITHM
If true, fast algorithm is used.
boolean false
--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
GATK version 4.2.2.0-SNAPSHOT built at Thu, 19 Aug 2021 09:49:28 -0700.
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