cnv_facets run problem

Question

[hamideh]

I used the cnv_facets package to obtain CNV between normal and diseased for cattle. I got the Fasta and VCF files from Ensemble. Each FASTQ file is about 2 GB in size, my data is whole genome. But in the output of the Excel file, I see only one chromosome. I run the following command:

cnv_facets.R -t 234h.sorted.bam -n 475.sorted.bam -vcf bos_taurus.vcf.gz -o output_prefi

Thank you for your guidance

Answer 1

[dariober]

cnv_facets currently supports only mouse and human genomes (I know...). I'm in the process of enabling other species, but for the time being you could use the original facets package.

[hamideh]

Yes, I know, but there was a command that can be used for other creatures by setting gc. Thanks for your guidance