Closed MikeWLloyd closed 4 months ago
Hi, based on your first BAF plot, the data have large LOH regions in those narrow chromosomes. Without normal samples, it is a bit hard to identify those LOH regions. You could try to customize parameters in the platform based on https://github.com/VanLoo-lab/ascat/issues/73 to rescue segments within the LOH region. We are working on an updated version to deal with this situation, but not release yet.
Thank you for the reply. Having this understanding to explain the patterns is a big help. I will see if I can rescue any region based on #73, and if not keep an eye out for the next release.
I am trying to understand why I am seeing different chromosome widths in the profile plots across samples (and in general). I have tried to look through documentation and methods papers, but can not find information on this. I am running tumor-only Illumina Cyto-SNP v2.1 data with GC and RT files I've made from the Illumina manifests. I am also running predictGermlineGenotypes as:
gg = ascat.predictGermlineGenotypes(ascat.bc, platform = "IlluminaCytoSNP")
.Below is an example plot with compressed widths. Can you provide details on what drives the patterns I am seeing?