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If we are using our own bed file with CNV calls(not using CNVKit), do we need to call cnv_prefilter or is using amplified_intervals.py enough? What additional filtering does cnv_prefilter do?
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## Bug Report
### Affected tool(s)
HaplotypeCaller
### Affected version(s)
latest GATK4
### Description
A user reported a verified 50 bp insertion is not being called with HaplotypeCaller…
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Hi ! thanks for your work, i would like to know if it's possible to add CNV/SNV on the plot? thanks :)
i'm using:
python 3.8
pyGenomeTracks 3.7
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hi @marcelTBI
I now only have the raw reads count of each bin,which hg19 genome are you using? can you give me a download url ? I want to use the trained means file(npy) you built, so i should …
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For example, we can represent CIViC variant amplification records as Copy Number Change
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I have adjusted the CNV using calculate-cnv, segment-cnv, and correct-cnv. After that, I was trying to see in the triangular plot of the cool file at the same region. Basically, it calculated chr5 at …
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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 all
Self explanatory hopefully. We have got a germline adaptive sampling panel working on Nanopore, and are generating copy number variants and SVs (including fusions) - do you think there is an…
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why i usually get invalid mutation 'All reads is filtered in this scope, total & filtered reads num 3716'
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Hi all,
I'm trying to use the final infercnv.obj to make a cnv plot, but get a error. "Error in rep(contig_name, contig_tbl[contig_name]) :
invalid 'times' argument". anyone counld help me to fix…