Writes an interval list based on splitting a reference by Ns. This tool identifies positions in a reference where the bases are 'no-calls' and writes out an interval-list using the resulting coordinates. This can be used to create an interval list for whole genome sequence (WGS) for e.g. scatter-gather purposes, as an alternative to using fixed-length intervals. The number of contiguous nocalls that can be tolerated before creating a break is adjustable from the command line.
java -jar picard.jar ScatterIntervalsByNs R=reference_sequence.fasta OT=BOTH O=output.interval_list
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.