Eric Roller

I'm hitting this same error on Ubuntu 18.04 (WSL) with python3.8. I've installed cyvcf2 0.20.9 using pip. I have a successful install of cyvcf2 on centos7 and running ldd on...

Thanks. I confirmed that works. I also installed cyvcf2 to my site python3.8 site packages using `CYTHONIZE=1 pip install -e .` as mentioned in the README so that cyvcf2 could...

Thanks for pointing this out. It seems like we should make --ploidy-vcf a required parameter then. If you don't care about proper sex chromosome calling for a male sample, you...

Here is a template ploidy vcf for a female sample using Grch38 : ``` ##fileformat=VCFv4.1 ##INFO= ##FORMAT= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HCC1187-NovaSeq-Grch38 chrY 0 ....

Yes, the file should contain the sex chromosome ploidy of the normal sample. Canvas estimates tumor sample purity and overall ploidy (e.g. 4 for a tetraploid tumor) from both coverage...

What reference genome are you using? As long as the coordinates are the same you should be able to use one of the existing kmer.fa files we provide and simply...

We provide normalized coverage values for each bin in bigwig format. Look for `coverage.bigWig` in the per-sample temp sub-directory under the analysis output directory. the bigwig file contains floating point...

I agree it is confusing. Perhaps there is better terminology for these "required options" (maybe "named arguments" would be better since these are more closely related to "positional arguments"). Python's...

Yes, genome.fa contains the same sequence (minus chrM and alternate/unplaced contigs) as kmer.fa. Off the top of my head you might even be able to just copy kmer.fa and use...

what platform are you on? dotnet 1.x is available for download for these systems: https://docs.microsoft.com/en-us/dotnet/core/linux-prerequisites?tabs=netcore1x. If you are on an incompatible OS you can try running it through a docker...