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Old 05-10-2019, 01:18 AM   #4
vivek_
PhD Student
 
Location: Denmark

Join Date: Jul 2012
Posts: 164
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I'd suggest raising an issue on the GATK support forums. One of the other issues I had been encountering with GATK4 is that there is a discordance between the command line options in the online documentation and what the tool actually expects, I've often had to search through their forums to find other such issues to fix my commands. The rollout of GATK4 has been far from smooth.
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