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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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Check Bin220 VAF histograms for all AD7 samples #41

Closed snurk closed 5 years ago

snurk commented 5 years ago

Reads: /mnt/gpfs/Hackathon/AD7_Complete/cutadapt/

snurk commented 5 years ago

In progress...

snurk commented 5 years ago

Extended dataset seems to be more interesting with respect to this bin! See png files in /mnt/gpfs/Hackathon/AD7/bin_analysis/bin_of_interest/dom/Bin_220

chrisquince commented 5 years ago

Yes although I am confused as sample12 here we see more complexity in variant frequencies than before but this is the same sample in fact that we did the nanopore for AD7 Week 24?

chrisquince commented 5 years ago

By the way should we add this variant frequency analysis to STRONG?

snurk commented 5 years ago

No :)

snurk commented 5 years ago

Let me check the controversy with sample12. Which sample should it correspond to in our original set of samples?

chrisquince commented 5 years ago

sample4

snurk commented 5 years ago

I think the difference comes from using the varscan on all the samples simultaneously. So when we have more samples it considers more of the rare variants as real rather than originating from sequencing errors, because they become confirmed by variants from other samples. Apart from the peak of rare variants the plots look the same :)

sample4 cov sample4 vaf sample12 cov sample12 vaf