Atlas-CNV
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theodorc
Method to detect exonic CNVs in NGS Gene Targeted Panels
Hi,Ted when I want to use Atlas-CNV for my target sequence data, I get some result files. They are sample_id.cnv.FAILED_sampleQC_and_sampleANOVA or sample_id.cnv.FAILED_sampleQC. Do they mean that these results are failed?...
Where can I find more information on how to create the panel and the sample fies? I went through the [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752313/pdf/41436_2019_Article_475.pdf) and it says - (1) Genome Analysis Toolkit (GATK)...
Hello, I've been getting the following error messages for every sample in my list: cp: cannot create regular file ‘/62209052_S14-ready.DATA.sample_interval_summary’: Permission denied cp: cannot stat ‘testmidpool’: No such file or...
R3.1.1
Dear Ted, Thank you very much for developing this tool. I tried to run Atlas-CNV on our cluster here at the NIH, but unfortunately, R3.1.1 is not supported anymore on...
https://github.com/theodorc/Atlas-CNV/blob/673a8e741c06e15a8612ba295bf7ff56e8c38774/convert_GATK_DoC.R#L39 Dear authors, Could you tell the reason that you choose 100 as the average read length? I got data that was sequenced by pair-end mode, is it ok to...
Dear authors, I want to use your software to call CNV in a targeted-gene panel. But I have a problem when I execute this command to run the atlas_cnv.pl script...
Dear authors, Is it possible for you to make available some test datas in order to test if everything is working well with my installation and my input files ?...
Hi, I tried to run Atlas-CNV and I was getting and error that has not been reported yet in the **atlas_cnv.R** script, in the `plot_cnvs()` function. The pipeline was working...
