Eric Talevich

Looks like CentOS 8 is past end of life, so dependency resolution will get trickier as time goes on. Another option you can try besides conda is the prebuilt Docker...

For HPC usage, you may also find conda or podman can avoid problems in the global environment.

You could try the `bintest` command to get a .cns of exon-level calls, then `export vcf` that. (If it doesn't work, please let me know. It ought to work, but...

Strange, it looks like in the `coverage` command, there are rows in the output of `samtools depth` (or pysam/htslib equivalent) that are parsed as in NA or Inf values. Are...

Thanks for the details, @amora197 . CNVkit can read GFF directly; you can give a GFF3/GTF/GFF2 file as input in most places where BED works. You can use the bundled...

Thanks for letting me know. I'll see about handling this case better. In the meantime, you can specify the y-axis lower limit with the `--y-min` option. You can also save...

For WGS, definitely use `segmetrics` and `call` to filter by CI. Then it may be more practical to use `bintest` or `genemetrics` to extract only focal CNVs or those that...

@gorgitko Ideally it should work if you use a mix of male and female normal and tumor samples all together in a single batch. Watch the status logs to see...

The Nexus spec refers to "word" and "punctuation" frequently and gives examples, but never gives a definitive listing or states whether a hyphen is punctuation. However, it does comprehensively list...

So! Even though hyphens are apparently allowed as taxon names in the NEXUS spec, the Bio.Nexus parser uses the same list of punctuation characters for parsing the entire NEXUS file,...