Eric Talevich
Eric Talevich
Thanks @28rietd , I've fixed this line in the Dockerfile: 39ea22952a0ef3c221062b7e815b29152cd0be91
... and I've pushed the 0.9.9 image containing the fix to Docker Hub here: https://hub.docker.com/repository/docker/etal/cnvkit/general#
Hi Felix and Siva, thanks for your attention to this. I like the solution of specifying the thresholds in `params.py` to ensure they're used consistently across the analysis (#753), rather...
It looks like you had some `NaN`-valued weights, or maybe log2 values. Which version of CNVkit are you using? If it's a very recent development version, there could have been...
Thanks for the details. Are you able to see if any of the input .cnr files contained NaN values? The test files bundled with CNVkit do not have NaNs, but...
I've merged a PR that should fix this issue. Could anyone try rerunning with the latest development version of CNVkit to see if the bug is resolved?
The ideogram does not behave well for WGS samples since there tends to be too much information to show on one plot. You can try the `--min-probes` option to limit...
Hmm, could be a bug. Thanks for reporting!
Yes, that's true. CNVkit doesn't tend to give useful calls on alternative contigs; read mapping is inconsistent. Here's the filter applied to sequence names in the commands `access` and `antitarget`:...
Are the high log2 ratios in the bin-level data (.cnr files) or segments (.cnr files)? Were the ratios high for all data points, or just a few? If you can...