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  • You have the CombineVariants argument --genotypemergeoption set to REQUIRE_UNIQUE, which produces the result you posted. Here is the documentation. --genotypemergeoption / -genotypeMergeOptions ( GenotypeMergeType ) Determines how we should merge …
  • Human error. I had a -L 20 argument in the command that I did not want, but somehow got in (cut and paste?). That is so human and makes me feel so stupid. But it is just the way we are built. We humans see what we expect.. This is exactly why GATK e…
  • I did not write a clear question. Sorry. When I use the walker -T CombineVariants, I want all of the variants from all of the files in the new file. For simplicity imagine I am combining three files each with one individual, when only one of these f…
  • Yes that answers my question.
  • Alright you have not heard of this before and believe that both -o and --out are the same. I will double check to make sure I did not have a typo. I will let you know if the problem persists. Otherwise consider it closed.
  • No there is never enough time. I recognize that in the entire set of GATK (manuals, this forum, and programs). You are under tight budgets as are we all, have heavy works loads, and want to maximize your output. All of which leads to understandable …
  • yes it did. Although I now have the images they are still not in the .pdf file. I will work around this. Thanks.
  • Wow you are fast. I am on a Windows 7 PC with full Adobe Acrobat, not just the reader. You solved my problem. Using just the reader the links go live. I guess the "Professional" version is not a good as the amateur version. Thanks.
  • Please do that. If on page 2 below the current content you place a red box with something like Table of Contents found on page 330 it would be a great boon to other newbs. Adobe is idiotic for doing it this way. Every technical book I have read, and…
  • Strange thing. What corruption will allow the data to run through -T CountReads but not run through -T CountLoci?