The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
I run into the errors below, when I try to run the StructuralVariationDiscoveryPipelineSpark to discover structural variants in a given sample:
ERROR Executor: Exception in task 0.0 in stage 5.0 (TID 50)
java.lang.IllegalArgumentException: provided start is negative: -36
I am not sure why the tool has to throw up these errors when every other thing seems fine. I wiil appreciate if you could shed some light on this.