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

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Please see the WgsMetrics documentation for detailed explanations of the output metrics.

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Category Diagnostics and Quality Control

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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
 

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Please see the WgsMetrics documentation for detailed explanations of the output metrics.

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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	null	Input SAM or BAM file.
--OUTPUT  -O	null	Output metrics file.
--REFERENCE_SEQUENCE  -R	null	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	null	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	null	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 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.
--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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--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]

---

--arguments_file / NA

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

List[File]  []

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--COMPRESSION_LEVEL / NA

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

int  5  [ [ -∞  ∞ ] ]

---

--COUNT_UNPAIRED / NA

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 / 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

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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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--INCLUDE_BQ_HISTOGRAM / NA

Determines whether to include the base quality histogram in the metrics file.

boolean  false

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--INPUT / -I

Input SAM or BAM file.

R File  null

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--INTERVALS / NA

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

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--LOCUS_ACCUMULATION_CAP / NA

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 / 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_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

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--QUIET / NA

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

Boolean  false

---

--READ_LENGTH / NA

Average read length in the file. Default is 150.

int  150  [ [ -∞  ∞ ] ]

---

--REFERENCE_SEQUENCE / -R

Reference sequence file.

R File  null

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--SAMPLE_SIZE / NA

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

int  10000  [ [ -∞  ∞ ] ]

---

--showHidden / -showHidden

display hidden arguments

boolean  false

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--STOP_AFTER / NA

For debugging purposes, stop after processing this many genomic bases.

long  -1  [ [ -∞  ∞ ] ]

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--THEORETICAL_SENSITIVITY_OUTPUT / NA

Output for Theoretical Sensitivity metrics.

File  null

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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_FAST_ALGORITHM / NA

If true, fast algorithm is used.

boolean  false

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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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--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.