Eric Talevich
Eric Talevich
Could be related to #876
It could be under-correcting for GC and repeats overall. My aim in that commit was to improve performance on bins with extreme GC, where e.g. Picard showed there was still...
Sure, I can add that. The `batch` example is essentially the same either way -- you provide case and control BAM files, and the pipeline constructs a pooled reference from...
Yes, you can, but I'd recommend interpreting the results cautiously. The results on WGS without a robust reference built from a pool of control samples tend to be too noisy...
I've pushed the 0.9.9 image to Docker Hub: https://hub.docker.com/repository/docker/etal/cnvkit/general#
This error is about CNVkit's `reference.cnn` file, not the FASTA reference genome sequences. If you used `-r` with an existing file, then you don't need to (and shouldn't) also use...
I've merged @Zhu-Ying 's pull request. Are you able to try your analysis of this sample again with the development version of CNVkit, @qzhqzh ?
Thanks for the report. According to pandas-dev/pandas#45321 it looks like the fix is to use `items` in place of `iteritems`.
In the scatter plot I see some datapoints supporting single-copy losses at the ends of chr1, chr6, and chr7, and possibly chr17 and chr21. It's suspicious that they're at the...
Yes, those are reasonable filters. Exporting to VCF from the `.call.cns` file should generally be OK if you're happy with the filters that went into the `.call.cns`. You might want...