Eric Talevich
Eric Talevich
Hmm. In the .cns emitted by segmetrics, is there another column generated with a name similar to "sem"? If the column names diverged, that would be a simple bug to...
To specify a non-default R installation, try `cnvkit.py batch --rscript-path ~/my/r/folder/` where the argument is the R executable indicated by your `~/.Rprofile`, wherever that may be. I'll see about `--no-restore`...
That makes sense, thanks. I'll switch `--vanilla` to `--no-restore --no-environ` and roll a new release.
I've switched `--vanilla` to `--no-restore --no-environ` so that .Rprofile library paths will be respected. Does it work for you now?
Fixed here: https://github.com/etal/cnvkit/pull/911 Does installation work for you now?
I agree that doesn't seem correct. Could you share the relevant portion of this .cnr file? One possibility is that the SNPs in this segment were rejected by CNVkit for...
Could be bit rot. Some experimentation showed that even low-quality mappings provided a slightly better copy number signal than removing those reads, so filtering on quality isn't recommended anymore. But...
Related: https://github.com/etal/cnvkit/pull/912
Likely fixed in https://github.com/etal/cnvkit/pull/912. Can you try the latest development version and see if it works for you now?