Luc Marchand
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Thanks both for the answers. I will test those new switches / features as soon as I can.
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More info on the subject. I had followed the steps described here: https://gatk.broadinstitute.org/hc/en-us/articles/4407897446939--How-to-Run-germline-single-sample-short-variant-discovery-in-DRA...
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The google links seems obsolete. The reference hash table files are not there either.