Sections 7 to 10 are a list of dot points and I would like to see the details added. A collaborator is considering using Infinium MethylationEPIC arrays for cutaneous squamous cell carcinoma. But, the somatic mutation burden is high (mean 300 mutations per megabase) and almost always C to T caused by sunlight. I was hoping to read some insights in 7 SNPs and Other Issues. I wonder if minfi could accept a somatic VCF, such as created by Mutect 2, and automatically filter positions which were never Cs. My collaborator has matched whole genome sequencing on the same set of cancer samples. It's concerning that numerous melanoma journal articles we've found have done analysis on defauilt settings and ignored SNPs in another sunlight-driven cancer type.
BarryDigby
commented
2 years ago
Sections 7 to 10 are a list of dot points and I would like to see the details added. A collaborator is considering using Infinium MethylationEPIC arrays for cutaneous squamous cell carcinoma. But, the somatic mutation burden is high (mean 300 mutations per megabase) and almost always C to T caused by sunlight. I was hoping to read some insights in 7 SNPs and Other Issues. I wonder if minfi could accept a somatic VCF, such as created by Mutect 2, and automatically filter positions which were never Cs. My collaborator has matched whole genome sequencing on the same set of cancer samples. It's concerning that numerous melanoma journal articles we've found have done analysis on defauilt settings and ignored SNPs in another sunlight-driven cancer type.