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I added label.dist=0.0000001 with the hope it would bring labels together but didn't happen. Is this a bug?
Not only are they too spaced out, but they overlap with other regions. Is there a way to r…
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Hi,
I am trying to use CLAMMS to make cnv calls to my targeted panel NGS data. All steps went well except the last step with call_cnv. My bam files are mapped to ucsc hg19, so all chromosomes are s…
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Hi,
First thank you for this adaptation of conumee.
My colleagues and me get a brand new NextSeq 550 with EPICv2 array. So I've tried conumee2.0, but I got an error message:
CNV.import(arra…
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--Hi,
i have tested your tool and i obtain too much CNV, with GATK pipeline or CNVkit i obtain ~ 15 CNV whereas with Cobalt i have ~ 130 CNV. I don't know why ,i have used default parameters maybe …
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Hi,
@arpanda
When I use the golden data, I set `view.dG_range = [1000, np.inf]`, but a `deletion` is still being filtered out. Could you update the code to filter out only CNVs of type 'dup'? How…
xiucz updated
7 hours ago
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Hello!
I am running numbat on 36 lung tumor cryo visium reactions. My normal reference is a at tumor-adjacent "normal" visium reaction that has been confirmed to be tumor-free by a pathologist. My…
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Hi,
Thank you for this tool to summarize the copy number for multiple sample. It works great!
I got a question. In my CNV analysis for loss, we have only deletion or deep deletion, which is 1 or…
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in my suggestion, these would be invisible but functional, like when you have send/receive symbols in other iemguis.
This would make things more convenient and useful for abstractions (where conne…
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Hello working with several samples, all but 1 sample output the cnv.output.tsv. Have ran accucopy on this single sample many times, however no CNV output. Accucopy finishes with no error. Job finish…
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Hello,
I am trying to use the cnv_ltffinder2gff.pl and I keep getting this error:
```
stephenwyka@bspmgenomics:/data/wyka/transposable_elements/LM470$ ../../dawgpaws/scripts/cnv_ltrfinder2gff.p…