jkstrat
commented
3 years ago Hi maximus3219,
Thanks for you interest in CNV Radar. The error looks to be coming when we try to plot the data. It's trying to exponentiate the log2 fold change in read depth for plotting and it can't so it's crashing.
Can you tell me a bit more about the type of sequencing that you are using as an input to the tool. From the log file that you listed it appears that this is not whole exome sequencing. It looks like you only have 22 variants identified and only 4 of those pass the filtering steps (two on Chr5 and two on Chr7).
We built CNV Radar to address CNV calling on large targeted panels rather than small targeted panels. The validation testing that we performed was on larger targeted panels (whole exome) so I don't have any data to say how well the software performs on really small panels. If you have any samples with known truth, that would be something worth looking into further.
If possible, can you upload an example file (Tumor sample ROI summary and annotated VCF file) so I can take a closer look.
Regards, Jeran
maximus3219
I got the following errors when running CNV_radar.R
I followed the previous steps exactly as stated in the manual.
Please advise how I should fix the bug.
Thanks.
[2021-01-22 22:46:12] - readVCF - DEBUG - Reading in the vcf file /home/maximus/Documents/NGS/CNV_analysis/E6384_ann.vcf.gz [2021-01-22 22:46:12] - readVCF - DEBUG - 22 total variants reported in the VCF [2021-01-22 22:46:12] - readVCF - DEBUG - 22 variants reported on the autosomal or sex chromosomes [2021-01-22 22:46:12] - readVCF - DEBUG - 4 complex variants to remove from VCF [2021-01-22 22:46:12] - readVCF - DEBUG - 1 indels to remove from VCF [2021-01-22 22:46:12] - readVCF - DEBUG - 17 heterozygous and 0 homozygous variants reported [2021-01-22 22:46:12] - readVCF - DEBUG - Filtering VCF to only 'common' variants [2021-01-22 22:46:12] - readVCF - DEBUG - 4 variants annotated as common [2021-01-22 22:46:12] - readVCF - DEBUG - 4 total heterozygous common single nucleotide variants reported in the VCF [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 1 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 2 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 3 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 4 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 5 = 2 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 6 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 7 = 2 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 8 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 9 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 10 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 11 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 12 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 13 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 14 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 15 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 16 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 17 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 18 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 19 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 20 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 21 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome 22 = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome X = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - Variants reported on chromosome Y = 0 [2021-01-22 22:46:12] - readVCF - DEBUG - VCF file /home/maximus/Documents/NGS/CNV_analysis/E6384_ann.vcf.gz with 4 variants took 0.001 minutes to read and parse [2021-01-22 22:46:12] - main - INFO - Allele frequencies from GATK are biased above 250x depth, removing those positions. [2021-01-22 22:46:12] - readROI - DEBUG - Reading in the depth file /home/maximus/Documents/NGS/CNV_analysis/E6384_sorted_roiSummary.txt [2021-01-22 22:46:12] - readROI - DEBUG - ROI depth file /home/maximus/Documents/NGS/CNV_analysis/E6384_sorted_roiSummary.txt with 269 regions of interest took 0 minutes to read and parse [2021-01-22 22:46:12] - main - DEBUG - Filtering to autosomes only [2021-01-22 22:46:12] - main - DEBUG - Median normalizing iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Beginning modeling for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Calculating fold change for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 1 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 2 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 3 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 4 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 5 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 6 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 7 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 8 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 9 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 10 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 11 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 12 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 14 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 15 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 17 for iteration 1 [2021-01-22 22:46:12] - main - DEBUG - Analyzing Chr 19 for iteration 1 [2021-01-22 22:46:12] - genomePlot - DEBUG - Plotting the genome for iteration 1 Error in exp(depth$fc) : non-numeric argument to mathematical function Calls: plotCNV -> plot -> plot.default -> xy.coords Execution halted