Hi! I am relatively new to ChipSeq data analysis. Having worked in WGS data analysis, I am aware that it's wise to call Variants in alt aware manner, I am however unsure if same applies in PeakCalling or not (I also searched about alt aware peak calling but didn't get any result). I know from this article that Alternative loci are not meant to represent all variation within a population, but rather provide an immediate solution for adding sequences missing from the chromosome assembly. Keeping this information in mind, aligning reads in an alt unaware manner and then calling peaks might be misleading, I presume.
I learned bwa is the only tools currently that does read alignment in alt aware manner. I wish to know if there are more. Also, will alignment in alt aware manner hold relevance in Histone ChipSeq data analysis or not.
All kinds of inputs are welcomed.