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We support three types of interval lists, as mentioned here. Interval lists should preferentially be formatted as Picard-style interval lists, with an explicit sequence dictionary, as this prevents accidental misuse (e.g. hg18 intervals on an hg19 file). Note that this file is 1-based, not 0-based (first position in the genome is position 1).
One relatively easy way to combine your intervals is to use the online tool Galaxy, using the
Get Data -> Upload command to upload your intervals, and the
Operate on Genomic Intervals command to compute the intersection or union of your intervals (depending on your needs).
Geraldine Van der Auwera, PhD