Philip Mabon

So looks you can make them be included IF you set the minimum base pair quality to 0.

That would be great! Thanks for the info.

Hey Karel, The overall trick to have both SNV and non-SNV in the same vcf file is to run ococo 2 separate times. First time you run it, you pass...

@karel-brinda is there any plans to add this feature?

Unfortunately our computing cluster does not support docker yet.

We are moving toward using singularity and hope to be moved in the near future!

The output always contain a `.` character hence why it always works. It will not parse correctly when a file path has a `.` since it will start the split...