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Can HaplotypeCaller determine ploidy of an unknown sample?
I have NGS data from an organism that is sometimes found to be aneuploid (but usually diploid.) I am trying to determine the ploidy of the individual I have sequenced from my population of interest. I have ~100X coverage, but the best reference is so distantly-related that the normal SNP coverage plots that are used to estimate ploidy are too messy to interpret. I was hoping that I could use HaplotypeCaller here to help determine the number of haplotypes per chromosome (where 2 haplotypes/alleles per position indicates diploidy). I can't figure out how to interpret the resulting VCF file well enough to address this question.
If HaplotypeCaller will not be sufficient, are there any other frequently used options to determine ploidy (or number of alleles/haplotypes per position)?
Thanks for any assistance.