I have RNAseq data of a water buffalo based on which I have got SNV and INDEL information in a VCF file (all variants annotated as well). Is it possible to decipher allele specific expression information from such data? Unfortunately, I do not have their parental genome information. Any logical/methodological answers are welcome. I am doing such analysis for the first time.
Some more details: I have got read counts for my reference allele and alternate allele which I got after using allelecounter.py program (github). I am stuck after this step. There are a variety of papers which infers to a lot of methods but I am not sure which method to go ahead with. I know that I can infer about allelic imbalance by doing a binomial test (used python scipy package for that). But, if I do not have any parental genomes, is it possible to determine from which chromosome has a particular allele has come?