I am looking to inquire whether there are any tools available that take into account aneuploidy, ploidy, and CNV in a genome when filtering VCF files. I am looking to filter my VCF files so that the ABHet (allelic balance at heterozygous sites) falls within an expected threshold. For example, an ABHet > 0.3 for diploid genomes.
I do not want to exclude SNPs however that are within regions of the genome that contains aneuploidy or copy number variation. At these sites, I would expect a different ratio for ABHet. Some of the genomes I am working with also have different ploidy (triploid), and would also have a different expected threshold for ABHet.
Are there any available tools that take into account these factors when filtering VCF files, or am I stuck with hard filtering across the VCF file and excluding SNPs that fall into these regions?