Converts a BED file to a Picard Interval List. This tool provides easy conversion from BED to the Picard interval_list format which is required by many Picard processing tools. Note that the coordinate system of BED files is such that the first base or position in a sequence is numbered "0", while in interval_list files it is numbered "1".BED files contain sequence data displayed in a flexible format that includes nine optional fields, in addition to three required fields within the annotation tracks. The required fields of a BED file include:
java -jar picard.jar chrom - The name of the chromosome (e.g. chr20) or scaffold (e.g. scaffold10671) chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered "0" chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
INPUT (File) The input BED file Required.
SEQUENCE_DICTIONARY (File) The sequence dictionary Required.
OUTPUT (File) The output Picard Interval List Required.
SORT (Boolean) If true, sort the output interval list before writing it. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
UNIQUE (Boolean) If true, unique the output interval list by merging overlapping regions, before writing it (implies sort=true). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}