Category

Sam/Bam Manipulation


Usage

java -jar picard.jar CollectAlignmentSummaryMetrics R=reference_sequence.fasta I=input.bam O=output.txt


Manual

MAX_INSERT_SIZE (Integer)    Paired-end reads above this insert size will be considered chimeric along with inter-chromosomal pairs. Default value: 100000. This option can be set to 'null' to clear the default value.
EXPECTED_PAIR_ORIENTATIONS (PairOrientation)    Paired-end reads that do not have this expected orientation will be considered chimeric. Default value: [FR]. This option can be set to 'null' to clear the default value. Possible values: {FR, RF, TANDEM} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.
ADAPTER_SEQUENCE (String)    List of adapter sequences to use when processing the alignment metrics. Default value: [AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG]. This option can be set to 'null' to clear the default value. This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.
METRIC_ACCUMULATION_LEVEL (MetricAccumulationLevel)    The level(s) at which to accumulate metrics. Default value: [ALL_READS]. This option can be set to 'null' to clear the default value. Possible values: {ALL_READS, SAMPLE, LIBRARY, READ_GROUP} This option may be specified 0 or more times. This option can be set to 'null' to clear the default list.
IS_BISULFITE_SEQUENCED (Boolean)    Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
REFERENCE_SEQUENCE (File)    Reference sequence file. Note that while this argument isn't required, without it only a small subset of the metrics will be calculated. Note also that if a reference sequence is provided, it must be accompanied by a sequence dictionary. Default value: null.
INPUT (File)    Input SAM or BAM file. Required.
OUTPUT (File)    File to write the output to. Required.
ASSUME_SORTED (Boolean)    If true (default), then the sort order in the header file will be ignored. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
STOP_AFTER (Long)    Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value.


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