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Theresa Saunders

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  • Well, haha I figured out where everything was going wrong, and it was a really simple fix. In my original command, I just had to replace the & with ||.  Original: gatk VariantFiltration -R rorida_q...

  • Update: The problem seems to somehow be tied to the input file for the VariantFiltration step. In my case, it is Rorida_quinquenervia.SNPall.vcf. The VariantFiltration fails as soon as it come to a...