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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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Currently we assume that every variant is a focal change with a nucleotide `alt` sequence. This is only a subset of the VCF spec and doesn't allow us to load variants such as:
```
#CHROM POS ID RE…
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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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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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I am filtering a multi VCF file of > 1000 sapmples, to identify somatic variants. So, I want to include variants which achieve this criteria:
1) SNPs
2) Observed once or twice (minor allele frequ…
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In the context of somatic mutations there is no easy way to represent a genotype in the same way as in germline variants. For this reason, some somatic mutation callers, do not provide genotype inform…
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As an idea for a dataset with a "story", we could use mapping of diseases in dog breeds, which can be done with a simple filtering for fixed mutations in the disease group (kind of like a very simple …
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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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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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Hello,
I have RNASeq data (tumor and normal samples) and I'm using your pipeline to detect somatic variants. However, I encountered the following error while running the pipeline. Your assistance w…