I would like to know what methods are mostly used to extrapolate a LOH event from variant allele frequencies on SNPs. I have targeted sequencing data on FFPE tumors so that's the only approach I can possibly utilize. My current problems are
a) Finding a script (R?) that takes into account tumor cell content (%) b) Normalize my data (quantile?) as I have quite a few frequencies that don't aggregate in 0, 0.5 and 1 VAF.
Note that my samples include a normal site and a primary tumor for each case. Initially I tried to use Bioconductor's quantsmooth but couldn't figure out the right way to format my input.