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problem with idx files -> InvocationTargetException
To run any GATK program I need to delete idx file generated at previous step.
For example, Haplotype caller generate a file.g.vcf.idx file that need to be erased before calling GenotypeGVCFs.
If not the program end with an InvocationTargetException.
And the first thing the new program do is generate an idx file.
I'm used to it now so it's not a big problem, but I'd like to know if anybody has the same problem.
(I'm using GATK version 3.2.2)