Question: Liftover dbSNP IDs
0
gravatar for Arko
9 weeks ago by
Arko10
US/Boston/Boston University
Arko10 wrote:

I have a list of SNPs from dbSNP build 150, I want to run a batch analysis on SIFT which uses an older build of rsid's (build 138 - if I'm not mistaken).

I understand that dbSNP rsids are updated based to avoid synonymous occurrences, but could someone please clarify on how would I map the rsids to an older build which is required by SIFT?

Is there any way of confirming the build for my current list of IDs?

Can different genome assemblies have the same rsIDs?

snp assembly • 110 views
ADD COMMENTlink modified 9 weeks ago by Pierre Lindenbaum111k • written 9 weeks ago by Arko10
0
gravatar for Pierre Lindenbaum
9 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum111k wrote:

y on how would I map the rsids to an older build which is required by SIFT?

dbsnps is available for several builds:

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/

Can different genome assemblies have the same rsIDs?

yes e.g rs25

https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=25

GRCh38.p7   108 7   11544515    NT_007819.18    11534515    Rev T   Fwd view    mapup
GRCh37.p13  105 7   11584142    NT_007819.17    11574142    Rev T   Fwd view    blast
ADD COMMENTlink written 9 weeks ago by Pierre Lindenbaum111k
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