Just trying to quickly figure out if I'm wasting my time.
I have exome sequencing data from colorectal cancer polyps and I want to assess copy number using a R based pipeline ASCAT: https://www.crick.ac.uk/peter-van-loo/software/ASCAT.
The ASCAT software requires two inputs, BAF and LogR. In their description of the software they make reference to how to use attain these values from Illumina sequencing platforms and Affymetrix SNP chips. BAF is fairly self-explanatory, as it can easily be extracted from my VCF files. My issue is with the LogR value. From what I can tell it is a measure of signal intensity given by some (all?) sequencing platforms.
Our sequencing data was generated using a PGM Ion Torrent platform with Ampliseq. My question is, therefore, can I obtain these logR values somehow from the annotated BAM files I have from the PGM? Or am I wasting my time and should instead rely on another CNV caller than I know works with Ion torrent (e.g. CNVkit)?
I would really appreciate if someone could quickly write if CNV of PGM WES through this ASCAT package is even possible!