Thank you very much.
I am analysing the 1000G VCF files, rs80314515 is not available in the VCF, but rs10204648 is available.
dbSNP returns this message when I search rs80314515 (https://www.ncbi.nlm.nih.gov/snp/?term=rs80314515)
rs80314515 has merged into rs10204648
I wonder if there is a data base about which SNPs are merged? (For all the SNPs currently known)
And another issue is chr:pos for rs10204648 is chr2:85882623 according to dbSNP, but it is on chr2:86109746. Any idea what could be the reason? Is it different build?
1 answer
Firstly, the discrepancy that you observe with the position on chr2 is due to different genome reference builds:
- chr2:85882623 = GRCh38 / hg38
- chr2:86109746 = GRCh37 / hg19
Merging of records FAQ
Yes, the merging of records is more common than you may imagine. There is a FAQ on the merging of dbSNP rs IDs here: https://www.ncbi.nlm.nih.gov/books/NBK44468/
All merged dbSNP records
In addition, here is a search configuration that lists all dbSNP rs IDs that have been merged: https://www.ncbi.nlm.nih.gov/snp/?term=mergedrs (the option to download the data is on that page - see 'Send to' at top-right).
Same dbSNP, multiple positions
You should also be aware that quite a few dbSNP rs IDs are duplicated and have different positions in the same reference genome build. Take a look at the reason here: https://www.ncbi.nlm.nih.gov/books/NBK44455/#Build.why_does_rs3823342_have_two_differ_1
Good luck and trust that this helps.
Kevin
Using the "Send to" function to download is very slow.
RsMergeArch.bcp.gz is available in the dbSNP FTP folder: ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/data/organism_data/
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