java -jar picard.jar

Reference

Computes a number of metrics that are useful for evaluating coverage and performance of sequencing experiments.

Category

Sam/Bam Manipulation

Usage

java -jar picard.jar CollectWgsMetricsFromQuerySorted

Manual

INPUT (File)    Input SAM or BAM file. Required.
OUTPUT (File)    Output metrics file. Required.
MINIMUM_USABLE_MAPPING_QUALITY (Integer)    Minimum mapping quality for a read to contribute to usable coverage. Default value: 20. This option can be set to 'null' to clear the default value.
MINIMUM_USABLE_BASE_QUALITY (Integer)    Minimum base quality for a base to contribute to usable coverage. Default value: 20. This option can be set to 'null' to clear the default value.
MINIMUM_RAW_MAPPING_QUALITY (Integer)    Minimum mapping quality for a read to contribute to raw coverage. Default value: 0. This option can be set to 'null' to clear the default value.
MINIMUM_RAW_BASE_QUALITY (Integer)    Minimum base quality for a base to contribute to raw coverage. Default value: 3. This option can be set to 'null' to clear the default value.
GENOME_TERRITORY (Long)    The number of bases in the genome build of the input file to be used for calculating MEAN_COVERAGE. If not provided, we will assume that ALL bases in the genome should be used (including e.g. Ns) Default value: null.

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