Extract OxoG metrics from generalized artifacts metrics.

This tool extracts 8-oxoguanine (OxoG) artifact metrics from the output of CollectSequencingArtifactsMetrics (a tool that provides detailed information on a variety of artifacts found in sequencing libraries) and converts them to the CollectOxoGMetrics tool's output format. This conveniently eliminates the need to run CollectOxoGMetrics if we already ran CollectSequencingArtifactsMetrics in our pipeline. See the documentation for CollectSequencingArtifactsMetrics and CollectOxoGMetrics for additional information on these tools.

Note that only the base of the CollectSequencingArtifactsMetrics output file name is required for the (INPUT_BASE) parameter. For example, if the file name is artifact_metrics.txt.bait_bias_detail_metrics or artifact_metrics.txt.pre_adapter_detail_metrics, only the file name base 'artifact_metrics' is required on the command line for this parameter. An output file called 'artifact_metrics.oxog_metrics' will be generated automatically. Finally, to run this tool successfully, the REFERENCE_SEQUENCE must be provided.

This command also lets you specify the detail metrics files by name, if files are not in the usual location or have different names. For example, the arguments PRE_ADAPTER_IN and BAIT_BIAS_IN specify the file location of the pre adapter detail metrics and the bait bias detail metrics respectively. If these arguments are provided then the value of INPUT_BASE is ignored.

Usage example:

java -jar picard.jar ConvertSequencingArtifactToOxoG \
     I=artifact_metrics \
     R=reference.fasta

Please see the metrics definitions page at ConvertSequencingArtifactToOxoG for detailed descriptions of the output metrics produced by this tool.

---

Category Diagnostics and Quality Control

---

Overview

ConvertSequencingArtifactToOxoG (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
Optional Tool Arguments
--arguments_file		read one or more arguments files and add them to the command line
--BAIT_BIAS_IN		The bait bias input file. Defaults to a filename based on the input basename
--help  -h	false	display the help message
--INPUT_BASE  -I		Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics). If this is not specified, you must specify PRE_ADAPTER_IN and BAIT_BIAS_IN
--OUTPUT_BASE  -O		Basename for output OxoG metrics. Defaults to same basename as input metrics
--OXOG_OUT		File for the output OxoG metrics. Defaults to a filename based on the output basename
--PRE_ADAPTER_IN		The pre adapter details input file. Defaults to a filename based on the input basename
--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.

---

--arguments_file

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

List[File]  []

---

--BAIT_BIAS_IN

The bait bias input file. Defaults to a filename based on the input basename

File  null

---

--COMPRESSION_LEVEL

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

int  5  [ [ -∞  ∞ ] ]

---

--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

---

--INPUT_BASE / -I

Basename of the input artifact metrics file (output by CollectSequencingArtifactMetrics). If this is not specified, you must specify PRE_ADAPTER_IN and BAIT_BIAS_IN

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  [ [ -∞  ∞ ] ]

---

--OUTPUT_BASE / -O

Basename for output OxoG metrics. Defaults to same basename as input metrics

File  null

---

--OXOG_OUT

File for the output OxoG metrics. Defaults to a filename based on the output basename

File  null

---

--PRE_ADAPTER_IN

The pre adapter details input file. Defaults to a filename based on the input basename

File  null

---

--QUIET

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

Boolean  false

---

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null

---

--showHidden / -showHidden

display hidden arguments

boolean  false

---

--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

---

Return to top

---

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