cnv_facets
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dariober
Somatic copy variant caller (CNV) for next generation sequencing
Hi, After I got help from @dariober , I finally runned cnv_facets sucessfully.Appreciate! The output included a plot. I have several questions: 1. why was the purity value NA in...
It would be great if the tool would output a ".seg" file that you can load into IGV. It's easy enough to parse the VCF but just some that that...
Hello, I have this message when I try to run cnv_facets : ``` Error in makeCluster(nprocs, type = "FORK") : could not find function "makeCluster" Calls: exec_snp_pileup_parallel Execution halted ```...
Hi, I tried installing `cnv_facets` through conda as specified, but I am running into an issue when running the calling: ``` (facets) [vym1@compute-e-16-198 facets]$ cnv_facets.R -h Error in library(argparse) :...
Hi, is there a way to annotate facets output and obtain information about copy number of each gene? I would like to obtain result similar to BRCA1 1 copy BRCA2...
Hello, I am trying to detect chromothripsis in some ovarian cancer data using the tool ShatterSeek (https://github.com/parklab/ShatterSeek). The tool takes in SV calls and CNV segments with TCN for each...
Hello, I installed cnv_facts via bioconda and i seem to getting the desired parameter info via --help. However whilst running on bam files; I get the following error - ```...
Hi. thank you for your effort with this script. I am just wondering if there is a way of installing r-facets 0.6.1 version with the 0.16.0 version of cnv_facets using...
Solid work here. Having VCF output puts this well ahead of other FACETS wrappers I've seen. `cnv_facets` currently uses FACETS `v0.5.14`. Do you have plans to update this? [Here is...
Hello dariober, I'm trying to run cnv_facets on Ubuntu but it doesn't work. `cnv_facets.R -t -n -vcf common_all_20180418.vcf.gz -o ` the error message like: `mkfifo: cannot create fifo ‘output.csv.gz_200520-155405_29956dc5eb59/common_all_20180418.1.vcf’: Operation...
