Using GATK 18.104.22.168.
I am getting the following error:
A USER ERROR has occurred: File /path/to/0049-scattered.interval_list is malformed: Interval file could not be parsed in any supported format. caused by Couldn't read file file:///path/to/0049-scattered.interval_list. Error was: file:///path/to/0049-scattered.interval_list has an invalid interval : hs37d5:1-35477943 + .
I use the Broad b37 reference (ie. Homo_sapiens_assembly19.fasta). I created this interval list using GATK's SplitIntervals script so I'm not sure why it would error out like this. Do you know why?
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