gnomAD AF & family-based vcf analysis

[XiaKwan]

Hi Xihao,

Thanks for your useful tool! And I've met some problems really confused me:

1. I noticed that allele frequencies of gnomAD and 1000G are contained in FAVOR full database but not in FAVOR essential database. Are there any approaches that I could make use of these AF annotations in the STAAR procedure? (Like the variants with gnomAD AF < 5‰ will be given priority).

2. I'm now working on a rare disease and my cohort contains ~700 trio families (only the child has the disease, parents are healthy), so my data is a vcf file with ~2000 samples. Does STAAR pipeline support family-based analysis? If so, how can I represent this family relationship while analyzing? (maybe in the pheno.csv?)

3. Do I need to add more irrelevant healthy samples as control?

Thanks a lot!!!