Manipulates interval lists. This tool offers multiple interval list file manipulation capabilities include sorting, merging, subtracting, padding, customizing, and other set-theoretic operations. If given one or more inputs, the default operation is to merge and sort them. Other options e.g. interval subtraction are controlled by the arguments. The tool lists intervals with respect to a reference sequence. Both interval_list and VCF files are accepted as input. The interval_list file format is relatively simple and reflects the SAM alignment format to a degree. A SAM style header must be present in the file that lists the sequence records against which the intervals are described. After the header, the file then contains records, one per line in text format with the following values tab-separated:
- Sequence name (SN) * Start position (1-based)** * End position (1-based, end inclusive) * Strand (either + or -) * Interval name (ideally unique names for intervals) The coordinate system of interval_list files is such that the first base or position in a sequence is position "1".
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