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Hi,
Thank you for developing this tool which is quite easy to use!
I am wondering if SpecHLA could also be used to detect somatic HLA mutations since we have paired tumor and normal WES or RNA…
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I've been trying to call somatic variants in a diploid organism, and so would like to set `--ploidy 4` for `nanopolish variants`. Whenever I do this, however, I get the following error:
```
nanopoli…
TimD1 updated
4 years ago
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Some variants only have Tier 2 reads supporting them but PASS. This results in the strange situation of having a passing somatic variant with a high EVS score in the filtered VCF file, but an allele f…
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`chr8 3671496 Minda_139 N . PASS SVLEN=78;SVTYPE=DEL;SUPP_VEC=PB_ID_45728_2,PB_severus_DEL7046,ILL_2186766853:2,PB_Sniffles2.DEL.B0M7,ILL_gridss139fb_11259h
`
https://v2.genomeribbon.com/?session=ht…
jzook updated
1 month ago
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**Describe the bug**
VarDict SVs once again end up in the SNV VCF files, making them hard to visualise for the user when loaded in Scout.
**To Reproduce**
Load e.g. case `novelbear` (or presumabl…
dnil updated
8 months ago
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**Describe the issue**
When running PureCN with my segmentation and VCF files, I encounter an error that says "Segmentation and VCF do not overlap." This stops the execution of the program.
**To R…
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Hello,
I am trying to get somatic mutations from `speedseq somatic` but it has been more than 24 hours but it is still running and no output is generated. Here is the command I am using:
tim…
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Hello,
I am using svtyper on the results of a lumpy somatic vcf and am therefore running it with 2 bwa-mem bams and 2 split reads bam files. I find that the progess is very slow at this point : ~200 …
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Hi, strelka team
I was really impressed by the model and performance of strelka in calling somatic mutations. But I have a question on the variant form in the vcf file. Can strelka report MNPs, com…
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Hi
I have tumor-only WGS, consisting of nodulous and tumorous tissue.
Your program is very interesting because filtering germline mutations in these samples have seemed very difficult and almost imp…