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How to build population frequency file based on GRCh38 for ContEst
This is Shenglai from the Univ of Chicago. Recently I have a question about how to build a population frequency file for ContEst. I visited CGA website, but there's limited information about how to build one on different ref. I have several following questions:
1. Can I use picard liftovervcf to upgrade provided hg19.hapmap3. input file to hg38? Although I tried and failed in this way, I was wondering if I did something wrong or it's not possible.
2. If not, Should I build the file on hapmap 2010-08_phaseII+III? There are allele and genotype frequencies, which one should I use? I noticed that in hapmap 2010-08, there are 11 population groups, but in ContEst provided hg19.hapmap3 file there are 17 population groups. Where can I find other groups' information or do I choose the wrong hapmap?
Any piece of advice would be helpful. Thank you.