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This can be caused by an incorrect invocation of the command or a malformed input file.
The SVGenotyper walker requires the GATK
-BTI argument, specifying the ROD which contains the input VCF file. Typically something like this:
-BTI input -B:input,VCF my_input_file.vcf
Another problem that can cause this same symptom is a malformed VCF input file. For example, if you have spaces instead of tabs in the VCF file, the GATK can fail to parse the VCF file and it can cause this error.
This can be caused by a malformed VCF file where the POS field is larger than the length of the chromosome. The "end point" value is the length of the chromosome.
Geraldine Van der Auwera, PhD