Is UNIQUIFY the default?
I want every variant in the output file with each individual in the same column
When you say three entries, you mean three separate lines, or one line with the three individuals' details? The default behavior is the latter.
Easiest way to check if it does what you want is to try it with a small VCF, and test out the different configuration options.
It's a little complicated because it depends on the value of the priority order argument. If you don't specify an option, the tool will check whether you specified a priority order. If yes, merging option will be set to PRIORITIZE. If not, merging will be set to UNSORTED.
If you want UNIQUIFY you have to specify it.
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 file has a variant, I want the resultant file to have three entries for that variant, showing the other two as calling 0/0. Does this walker do that? What options do I have to set to get it to do that?