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Hi. If I have performed data pre-processing step to filter out possiblegermline variants and only kept predicted somatic mutations, can the CBP2 of all variants be assigned a score of 1?
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We usually filter variants against a panel of normal samples. This can be done post variant calling by genotyping detected variants in this panel and call anything at a certain threshold in a minimum …
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Hi,
I'm currently evaluating VarDict on a synthetic tumour dataset similar to the ICGC DREAM set. I'm using VarDict version 1.5.2 with the following commands:
Call variants:
```shell
$ VarDi…
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e.g. B2M, TAP, &c.
Identifying loss in MHC might require running a custom program which first does genotyping of the germline MHC and then calls somatic variants against those specific alleles.
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Hi Jeremiah,
I have a question about the scores for somatic rearrangements. I was checking the detected variants in "*.svaba.somatic.sv.vcf" and was wondering whether "LO" in the FORMAT column is t…
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I want to use gemini to annotate my variants generated from GATK pipeline using hg38 genome. Below is the gemini version I'm using:
iit@iit:~$ /home/iit/bin/gemini -v
gemini 0.30.2
Installation:
…
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Due to their workflows taking too long. https://github.com/galaxyproject/training-material/pull/3293 comes to mind, but it seems the somatic variants tutorial also uses quite large datasets.
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At the moment we have "Global variant zygosity count" which is non-germline samples
We can support multiple ones, we just only have 1 at the moment
Need to work out what people would like to split b…
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ExAC allele counts and frequencies are already in the VEP cache. But we use the `ExAC_nonTCGA` VCF instead, minus a few known somatic variants related to hematopoietic clonal expansion. Figure out how…
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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…