dbSNP154

[AhmedArslan]

I am using MungSumstats package to standardize GWAS catalog data. MungSumstats uses dbSNP155 whereas at present GWAS Catalog uses dbSNP154, I wanted to ask how MungSumstats handles this issue?

Many thanks for doing great work.

best, Ahmed.

[Al-Murphy]

Hey @AhmedArslan,

You are right that this will affect any function used by MSS that uses the dbSNP reference dataset (which is quite a lot - look for any function calling load_ref_genome_data to get a list). However, and I haven't tested this but, I don't think there should be much change across dbSNP154 and dbSNP155 given the releases are so close so checks like check_on_ref_genome() shouldn't be affected by too large a degree. If you would like to test the effect though try running the on reference genome function (or any of the other checks using the reference genome) in isolation on a set of SNPs known to be dbSNP 154 and see how many are flagged as not on the reference genome. I would be really interested to see the results.

Thanks, Alan.