I am working with BAFsegmentation software (http://baseplugins.thep.lu.se/wiki/se.lu.onk.BAFsegmentation). I started with VCF files from exome sequencing, merged all sites and converted to a bed file. Then, I calculated b allele frequency at every site in this cumulative bed file for every sample and prepared a per-sample input file with corresponding Log R Ratios derived from a prior SCNA analysis.
The above program calculates allelic imbalance by performing segmentation using input B Allele Frequency or rather mBAF (mirrored B allele frequency--BAF reflected across the 0.5 axis) and Log R ratios for sites across the genome.
The output of this BAFsegmentation is very confusing. Could anyone tell me why I might observe mBAF segments at levels between 0.5 and 1 where copy number appears to be zero. Also, why do I observe peaks rather than longer segments. Would that make sense biologically?
Please let me know what additional files I can provide to help. Thanks!
If possible, can you show the raw minor allele frequency plot (using scatter plot format of the first figure)?