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.
java -jar picard.jar CollectOxoGMetrics I=input.bam O=oxoG_metrics.txt R=reference_sequence.fasta
INPUT (File) Input BAM file for analysis. Required.
OUTPUT (File) Location of output metrics file to write. Required.
REFERENCE_SEQUENCE (File) Reference sequence to which BAM is aligned. Required.
INTERVALS (File) An optional list of intervals to restrict analysis to. Default value: null.
DB_SNP (File) VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis. Default value: null.
MINIMUM_QUALITY_SCORE (Integer) The minimum base quality score for a base to be included in analysis. Default value: 20. This option can be set to 'null' to clear the default value.
MINIMUM_MAPPING_QUALITY (Integer) The minimum mapping quality score for a base to be included in analysis. Default value: 30. This option can be set to 'null' to clear the default value.
MINIMUM_INSERT_SIZE (Integer) The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads. Default value: 60. This option can be set to 'null' to clear the default value.
MAXIMUM_INSERT_SIZE (Integer) The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads. Default value: 600. This option can be set to 'null' to clear the default value.
INCLUDE_NON_PF_READS (Boolean) Whether or not to include non-PF reads. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
USE_OQ (Boolean) When available, use original quality scores for filtering. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
CONTEXT_SIZE (Integer) The number of context bases to include on each side of the assayed G/C base. Default value: 1. This option can be set to 'null' to clear the default value.
CONTEXTS (String) The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed. Default value: null. This option may be specified 0 or more times.
STOP_AFTER (Integer) For debugging purposes: stop after visiting this many sites with at least 1X coverage. Default value: 2147483647. This option can be set to 'null' to clear the default value.