Danny Antaki

To add... I've attempted to genotype SVs with `speedseq sv -g`using hg38 aligned genomes. I used an exclusion file that contained gaps, centromeres, and segmental duplications for hg38 and SVTyper...

Are you using python2? I think this error comes up when you try to install with python3

I think pybedtools will install bedtools if it cannot find the executable in the environment path. Not sure, will fix this with the next update of SV2. Thanks for all...

I can't replicate the issue, I did a clean `pip install sv2` in a new conda environment ``` (base) bucephalus@bucephalus:~$ conda activate py2test (py2test) bucephalus@bucephalus:~$ pip install sv2 DEPRECATION: Python...

Not sure how to include a local bedtools install without evoking conda. Any suggestions?

Does this mean CNVkit cannot call CNVs without a "control" panel? What if I want to make germline calls on a 30X whole genome for one sample at a time?