I am having trouble using DepthOfCoverage over a provided interval file. Although it runs fine if I omit the -L file.
The error that I get is:
A USER ERROR has occurred (version 1.3-20-g447e9bf): ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ERROR Please do not post this error to the GATK forum ERROR ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ERROR ERROR MESSAGE: File associated with name /Users/Desktop//myinterval.bed is malformed: Interval file could not be parsed in any supported format. caused by BED files must be parsed through Tribble; parsing them as intervals through the GATK engine is no longer supported
The format of the file is: chr1:XXXX-XXXXXX also tried 1:XXXXX-XXXXXX
Does anyone know what the problem might be? Is it the interval format? Thanks!