allelicBalance and checkHetsIndvVCF on WGS data

[npatel-ah]

Hello,

I've come across this informative article https://speciationgenomics.github.io/allelicBalance/ which brings me to the "allelicBalance" and "checkHetsIndvVCF" scripts.

As I read through the article it suggests that the script is not designed for WGS data but while reviewing the presentation here "https://github.com/speciationgenomics/presentations/blob/master/PDFs_2022/AllelicBalance_PCRduplication.pdf" it shows an example of WGS data.

What are the downsides of using the "checkHetsIndvVCF.sh" for WGS analysis? I am also curious how haploid individuals and the hard region of the genome like repeats will affect the results.

Regards,
Nihir