CollectOxoGMetrics (Picard)

Collect metrics to assess oxidative artifacts.This tool collects metrics quantifying the error rate resulting from oxidative artifacts. For a brief primer on oxidative artifacts, see the GATK Dictionary.

This tool calculates the Phred-scaled probability that an alternate base call results from an oxidation artifact. This probability score is based on base context, sequencing read orientation, and the characteristic low allelic frequency. Please see the following reference for an in-depth discussion of the OxoG error rate.

Lower probability values implicate artifacts resulting from 8-oxoguanine, while higher probability values suggest that an alternate base call is due to either some other type of artifact or is a real variant.

Usage example:

java -jar picard.jar CollectOxoGMetrics \
      I=input.bam \
      O=oxoG_metrics.txt \
      R=reference_sequence.fasta

Category Diagnostics and Quality Control

Overview

Class for trying to quantify the CpCG->CpCA error rate.

CollectOxoGMetrics (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 BAM file for analysis.
--OUTPUT -O	null	Location of output metrics file to write.
--REFERENCE_SEQUENCE -R	null	Reference sequence file.
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--CONTEXT_SIZE	1	The number of context bases to include on each side of the assayed G/C base.
--CONTEXTS	[]	The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.
--DB_SNP	null	VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.
--help -h	false	display the help message
--INCLUDE_NON_PF_READS -NON_PF	true	Whether or not to include non-PF reads.
--INTERVALS	null	An optional list of intervals to restrict analysis to.
--MAXIMUM_INSERT_SIZE -MAX_INS	600	The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.
--MINIMUM_INSERT_SIZE -MIN_INS	60	The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.
--MINIMUM_MAPPING_QUALITY -MQ	30	The minimum mapping quality score for a base to be included in analysis.
--MINIMUM_QUALITY_SCORE -Q	20	The minimum base quality score for a base to be included in analysis.
--STOP_AFTER	2147483647	For debugging purposes: stop after visiting this many sites with at least 1X coverage.
--USE_OQ	true	When available, use original quality scores for filtering.
--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.

--arguments_file / NA

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

List[File] []

--COMPRESSION_LEVEL / NA

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

int 5 [ [ -∞ ∞ ] ]

--CONTEXT_SIZE / NA

The number of context bases to include on each side of the assayed G/C base.

int 1 [ [ -∞ ∞ ] ]

--CONTEXTS / NA

The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.

Set[String] []

--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

--DB_SNP / NA

VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.

File 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_NON_PF_READS / -NON_PF

Whether or not to include non-PF reads.

boolean true

--INPUT / -I

Input BAM file for analysis.

R File null

--INTERVALS / NA

An optional list of intervals to restrict analysis to.

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 [ [ -∞ ∞ ] ]

--MAXIMUM_INSERT_SIZE / -MAX_INS

The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.

int 600 [ [ -∞ ∞ ] ]

--MINIMUM_INSERT_SIZE / -MIN_INS

The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.

int 60 [ [ -∞ ∞ ] ]

--MINIMUM_MAPPING_QUALITY / -MQ

The minimum mapping quality score for a base to be included in analysis.

int 30 [ [ -∞ ∞ ] ]

--MINIMUM_QUALITY_SCORE / -Q

The minimum base quality score for a base to be included in analysis.

int 20 [ [ -∞ ∞ ] ]

--OUTPUT / -O

Location of output metrics file to write.

R File null

--QUIET / NA

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

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

R File null

--showHidden / -showHidden

display hidden arguments

boolean false

--STOP_AFTER / NA

For debugging purposes: stop after visiting this many sites with at least 1X coverage.

int 2147483647 [ [ -∞ ∞ ] ]

--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

--USE_OQ / NA

When available, use original quality scores for filtering.

boolean true

--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

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GATK version 4.0.11.0 built at 23-11-2018 02:11:49.