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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 4.0.12.0 built at 09-29-2019 04:29:33.