Question: Pipeline for analysing multiple tumor/normal exome samples
gravatar for Nick
5.6 years ago by
Nick270 wrote:

I have a set of biological replicates consisting of multiple normal and tumor mouse samples. The samples are not matched (each sample corresponds to a different animal) but these are all mice from the same litter and are supposed to be genetically identical (apart from the somatic mutations in tumors). 

I am interested in a pipeline that would produce joint analysis of all samples. All the pipelines/tutorials I've seen are about single tumor/normal pairs. In theory, these can be re-used for multiple replicates by looking at overlapping mutations. But this seems to me to be a bit primitive. Also, in my case the samples are not matched so maybe it makes sense to consider some sort of cohort/pooled analysis. 

I am facing such an experimental design for the first time so would welcome any suggestions. 

tumor exome • 1.9k views
ADD COMMENTlink modified 5.6 years ago by donfreed1.5k • written 5.6 years ago by Nick270
gravatar for donfreed
5.6 years ago by
Mountain View, CA
donfreed1.5k wrote:

Try deepSNV. It is not built exactly for your situation but it might be more applicable than MuTect or Strelka.

ADD COMMENTlink modified 14 days ago by RamRS25k • written 5.6 years ago by donfreed1.5k
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