remaping rs386000 from GRCh38 to GRCh37.p13 using NCBI remap_api.pl
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6.9 years ago
burcakotlu ▴ 40

Hi,

I have tried to remap  rs386000 from GRCh38 to GRCh37.p13 using NCBI remap_api.pl.

From dbSNP, I can see that

rs386000's position in  GRCh38    is    chr19    54288907 and in GRCh37.p13   is    chr19    54792761;

however remap_api.pl returns NW_004166865.1:263274.

Why not chr19    54792761?

Any idea?

Thanks,

Burçak

NCBI REMAP rs386000 from GRCh38 to GRCh37.p13 • 2.5k views
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Hm, no idea, in general the SNP is not easy to map, and there are many remapping and patching issues, which you can retrace in dbSNP and ensembl:

http://www.ensembl.org/Homo_sapiens/Variation/Context?db=core;v=rs386000;vdb=variation

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=386000

Nevertheless the NW_004166865.1:263274 is a sequence which was removed from the database and replaced by another seq. Perhaps the script remap_api.pl  is accessing an old and not updated database?! It should use the sequence NT_011109.16 instead. Doing this the SNP has the correct position.

But why you actually want to "downmap" to an old build?

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