Category

Sam/Bam Manipulation


Usage

java -jar picard.jar ScatterIntervalsByNs R=reference_sequence.fasta OT=BOTH O=output.interval_list


Manual

REFERENCE (File)    Reference sequence to use. Required.
OUTPUT (File)    Output file for interval list. Required.
OUTPUT_TYPE (OutputType)    Type of intervals to output. Default value: BOTH. This option can be set to 'null' to clear the default value. Possible values: {N, ACGT, BOTH}
MAX_TO_MERGE (Integer)    Maximal number of contiguous N bases to tolerate, thereby continuing the current ACGT interval. Default value: 1. This option can be set to 'null' to clear the default value.


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