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With the above in mind, we are able to combine these two tables to obtain the relationship between older rs number and new rs number.
With the above in mind, we are able to combine these two tables to obtain the relationship between older rs number and new rs number.
We have developed a script (for internal use), named [http://genome.sph.umich.edu/wiki/LiftRsNumber.py liftRsNumber.py] AAAA for lift rs numbers between builds.
We have developed a script (for internal use), named [http://genome.sph.umich.edu/wiki/LiftRsNumber.py liftRsNumber.py] for lift rs numbers between builds.
This scripts require RsMergeArch.bcp.gz and SNPHistory.bcp.gz, those can be found in [[#Resources | Resources]].
This scripts require RsMergeArch.bcp.gz and SNPHistory.bcp.gz, those can be found in [[#Resources | Resources]].
Similar to the human reference build, dbSNP also have different versions. You may consider change rs number from the old dbSNP version to new dbSNP version
Similar to the human reference build, dbSNP also have different versions. You may consider change rs number from the old dbSNP version to new dbSNP version
depending on your needs. Such steps are described in [[#Lift dbSNP rs numbers | Lift dbSNP rs numbers]]. AAAA
depending on your needs. Such steps are described in [[#Lift dbSNP rs numbers | Lift dbSNP rs numbers]].
==== Method 2 ====
==== Method 2 ====
(2) Lookup SNP positions from rs number
(2) Lookup SNP positions from rs number
dbSNP provides a file [[#Resources | joinb132_SNPChrPosOnRef_37_1.bcp.gz]] which contains rsNumber, chromosome and its position.
dbSNP provides a file [[#Resources | b132_SNPChrPosOnRef_37_1.bcp.gz]] which contains rsNumber, chromosome and its position.
Use this file along with the new rsNumber obtained in the first step.
Use this file along with the new rsNumber obtained in the first step.
In practice, some rs numbers do not exist in build 132, or not suitable to be considered ( e.g. they do not reside on human reference, or they are mapped to multiple locations, these scenarios are noted by the chromosome column with values like "AltOnly", "Multi", "NotOn", "PAR", "Un"), we can drop them in the liftover procedure.
In practice, some rs numbers do not exist in build 132, or not suitable to be considered ( e.g. they do not reside on human reference, or they are mapped to multiple locations, these scenarios are noted by the chromosome column with values like "AltOnly", "Multi", "NotOn", "PAR", "Un"), we can drop them in the liftover procedure.
==== Method 3 ====
==== Method 3 ====
NCBI dbSNP team has provided a [[ #Resources | provisional map ]] AAAA for converting the genome position of a larget set dbSNP from NCBI build 36 to NCBI build 37.
NCBI dbSNP team has provided a [[ #Resources | provisional map ]] for converting the genome position of a larget set dbSNP from NCBI build 36 to NCBI build 37.
In the second step, we have obtained unlifted genome positions, so we can try to use the table to convert those unlfted dbSNPs.
In the second step, we have obtained unlifted genome positions, so we can try to use the table to convert those unlfted dbSNPs.
After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.
After this step, there are still some SNPs that cannot be lifted, as they are mostly located on non-reference chromosome.
Please contact [mailto:zhanxw@umich.edu Xiaowei Zhan].
Please contact [mailto:zhanxw@umich.edu Xiaowei Zhan].
