Category

Sam/Bam Manipulation


Usage

java -jar picard.jar CollectRawWgsMetrics I=input.bam O=raw_wgs_metrics.txt R=reference_sequence.fasta INCLUDE_BQ_HISTOGRAM=true


Manual

MINIMUM_MAPPING_QUALITY (Integer)    Minimum mapping quality for a read to contribute coverage. Default value: 0. This option can be set to 'null' to clear the default value.
MINIMUM_BASE_QUALITY (Integer)    Minimum base quality for a base to contribute coverage. Default value: 3. This option can be set to 'null' to clear the default value.
COVERAGE_CAP (Integer)    Treat bases with coverage exceeding this value as if they had coverage at this value. Default value: 100000. This option can be set to 'null' to clear the default value.
LOCUS_ACCUMULATION_CAP (Integer)    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 Default value: 200000. This option can be set to 'null' to clear the default value.
INPUT (File)    Input SAM or BAM file. Required.
OUTPUT (File)    Output metrics file. Required.
REFERENCE_SEQUENCE (File)    The reference sequence fasta aligned to. Required.
STOP_AFTER (Long)    For debugging purposes, stop after processing this many genomic bases. Default value: -1. This option can be set to 'null' to clear the default value.
INCLUDE_BQ_HISTOGRAM (Boolean)    Determines whether to include the base quality histogram in the metrics file. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
COUNT_UNPAIRED (Boolean)    If true, count unpaired reads, and paired reads with one end unmapped Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
SAMPLE_SIZE (Integer)    Sample Size used for Theoretical Het Sensitivity sampling. Default is 10000. Default value: 10000. This option can be set to 'null' to clear the default value.
INTERVALS (File)    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. To restrict the calculation just to individual positions without overlap, please see CollectWgsMetricsFromSampledSites. Default value: null.


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