I am looking into pseudogene contamination in NGS, and am hoping to predict the presence of pseudogene reads aligned to functional genes on the reference genome. I aim to determine the likely haplotype of these reads, and based on the variants found within these haplotypes, determine which belong to the functional gene reads and which belong to the pseudogene.
My question is: is there an argument of something like HaplotypeCaller which produces the determined haplotypes? Something like --bamOutput or --bamWriterType?
Sorry if this doesn't make sense, my bioinformatics knowledge is not very strong.