David Jakubosky

Thanks for the reply, I think the issue occurred on a heavily used cluster node- I had only been setting aside 4gb of mem per job- this was generally successful-...

I wanted to add in this example as something I wouldn't expect after merging or pruning  this particular variant is found in mostly the same individuals, and overlaps >50%

Yes you understand correctly, I have the pysam 0.1.1 installed in its own anaconda env with the speedseq config pointing to this python install. If I source activate this env...

Thanks for the tip on the svtyper update! I want to note that running genotyping on its own works with svtyper 0.1.4 also, using pysam 0.1.1. For now I will...

Thanks for the feedback. I noticed the svtyper version in svtools genotype is 0.1.2, is this an issue? do you suggest genotyping all sets of calls using 1.4?

Hi @zeeev Thanks for all the info on this, these answers are very helpful. I think I follow almost everything you are saying here. I still have one question- when...

Thanks for the info! Is there a limit to how many VCFs can be merged with regards to memory concerns? On Tue, Oct 1, 2019 at 3:15 PM Zev Kronenberg...