I am trying to estimate gene level Allele Specific Expression (ASE) within each sample using QuASAR https://www.ncbi.nlm.nih.gov/pubmed/25480375.

I have RNAseq data from cows and for each animal I've produced vcfs with HaplotypeCaller (GATK)

QuASAR requires as input a file containing the following 10 fields:

1/Chromosome,2/Start position, 3/End position, 4/Reference allele, 5/Alternate allele, 6/SNP ID, 7/SNP allele frequency, 8/Number of reads mapping to the reference allele, 9/Number of reads mapping to the alternate allele, 10/Number of reads not mapping to either allele

In their github page (https://github.com/piquelab/QuASAR) they produce such file by processing a general snp bed file from 1KG http://genome.grid.wayne.edu/centisnps/1kgSnps.html that contains the allele frequencies for each SNP in the population. But they mention that this can be modified.

I am struggling to figure out which alternatives are there, specially since I am working with bovine data and I cannot find a file with the population allele frequencies (if someone knows about such file, please let me know).

Would it be an option to replace the population allele frequencies by the allele frequency estimated by HaplotypeCaller for each individual?