What'S The Most Comprehensive Listing Of Hapmap Snps?
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12.6 years ago
Shigeta ▴ 470

The HapMap data is pretty old and new genome build has changed.
Can we use the dbSNP records themselves to get a hapmap inventory alignment with the newest dbSNP build?

I see records like this:

VAL | validated=YES | min_prob=? | max_prob=? | notwithdrawn | byCluster | byFre

quency | byHapMap

if Hapmap Validated a snp, and its not retired does this indicate it was used by HapMap in a study? We're not concerned what phase of HapMap used the data... I hope that is not a problem ?

dbsnp hapmap • 2.1k views
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Entering edit mode
12.6 years ago

yes, I guess you can solely rely on dbSNP to have a decent and useful HapMap inventory if you look for "byHapMap" validation, IF you have in mind that when HapMap batch uploads their findings to dbSNP they are filtered and curated. the important thing to consider is that HapMap uses dbSNP b126 to assign the rs codes, so if you get the data from dbSNP you will probably have slightly smaller number of SNPs than the ones you would get from HapMap due to that curation steps at dbSNP that include SNP merging and removing across different builds.

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Thanks Jorge! Yes we're hoping for a GRCh37 version of hapmap, so the filtering should be appropriate...

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