I have run CREST on all samples. See notebook for details.
The results were full of noise, i needed to postprocess them. See notebook for details and results.
Postprocessing and results
False positive mutations in Varscan
Indel proximity filtering test in DS014
IGV+pileup of strong SNPs in Sample4 IGV+pileup of strong SNPs in DS14
SNP spectra using varscan
Running varscan on all samples Varscan somatic filter bug
Phylogeny tree construction based on SNPs
het positions mpileup
low frequency positions mpileup
WT vs all mutations
Pileup and List creation
Varscan test version 0.1