Hello!
I know there has been quite a few posts in the pasts about this but I am still quite unsure so would like some advice!
I have two rare SNPs ( both are around 0.001966 AF in GnomAD V4.0) and want to see if they are likely on the same haplotype. They are both on GnomAD but their incidence as the alternate allele is not seen many times in V2.1 on the variant co-occurance calculator.
Using GnomAD co-ooccurance calculator if they are on the same haplotype, why are they not present in that middle column?
I did use LDpair prior but only 3 and 1 variants were present in the 1000 genomes dataset which it uses thus I am unsure if this would be reliable information.
Does anyone have any advice on being able to determine if these are on the same allele, or whether you would trust what both of these tools are saying?
