This question follows the previous question I posted on ResearchGate (please see the attached link).

I am now thinking of supplementing my EHH and rEHH and several other population genetics analyses test using the GEO Datasets available on NCBI. But, almost all of these sequence data are from ChipSeq and RNAseq. I know there will be bias and gaps in the variants obtained from these data but I am not looking for enriched regions, rather just want to collect polymorphism from the reads mapped with high quality (and non-enriched regions will be equally helpful).

Could someone please suggest me the pros and cons of taking this approach? Also, is there any methodology that can take this kind of data for population genetics analyses.

Note: I have high coverage whole genome sequence data from 6 individuals/population for two different populations.

Thanks in advance,

https://www.researchgate.net/post/Is_the_sample_size_of_6_genome_reseq_data_populations_enough_for_EHH_Extended_Halptotype_homozygosity_test_or_something_similar