Snp Position In Different Built

Question

[Omid]

I am working with GenomeStudio and studying SNPs within some specific genes. There are two built in the GenomeStudio program (Built 36.1 and built 37). I am wondering when I change the built and check specific SNPs, their positions do not change. That means we have a SNP at the same position in two different built, while I think the position should shift.

[Michael]

I would check the SNP position in dbSNP or Ensembl Variation Biomart and see if it is correct in your software.

[Omid]

I really appreciate Michael

Answer 1

[ff.cc.cc]

From Build_n to Build_n+1 there is NO guarantee to retrieve the same positions for the same SNP.

Usually the default is: everything change, even the rsID could be merged with another and suppressed.

-Suggest you to update all your marker positions to a reference like hg18/19 @ UCSC and work with them.

-Pay attention with outdated online tools

Answer 2

[Pierre Lindenbaum]

You can check if your SNP has moved with the following mysql query:

 $ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A \
   -e 'select H.name,H.chrom,H.chromStart,K.chrom,K.chromStart from hg19.snp132 as H ,hg18.snp129 as K where H.name="rs25" and K.name=H.name'
+------+-------+------------+-------+------------+
| name | chrom | chromStart | chrom | chromStart |
+------+-------+------------+-------+------------+
| rs25 | chr7  |   11584141 | chr7  |   11550666 |
+------+-------+------------+-------+------------+