remaping rs386000 from GRCh38 to GRCh37.p13 using NCBI remap

remaping rs386000 from GRCh38 to GRCh37.p13 using NCBI remap_api.pl

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10.0 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

REMAP NCBI • 3.2k views

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 10.0 years ago by burcakotlu ▴ 40

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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.

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?

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 9.9 years ago by Jimbou ▴ 960

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