rs number conversion when performing liftover from hg18tohg19

Question

[giulia.pagani]

Hello,

I used LiftOver to lift the Genome Position from hg18 to hg19. In order to convert the rs number, I looked at the following tutorial, and used their available python script (which uses Use RsMergeArch and SNPHistory). This produced a list of new snps, some lifted, unlifted or just unchanged. However it is not clear to me how I should proceed at this point, and/or this list is then used together with the data file b132_SNPChrPosOnRef_37_1.bcp.gz (a data file containing each dbSNP and its positions in NCBI build 37) to adjust the .map and .ped files accordingly (as stated in the method 2 of the above cited tutorial).

Any suggestions would be highly appreciated!

Thank you!

Giulia

[Kevin Blighe]

In the tutorial, they already provide specific instructions for updating rs IDs in the PLINK map and ped files, right (see 'Lift Merlin/PLINK format')? This is separate from the other section whose instructions you have already followed ('Lift dbSNP rs numbers') If it were I, I would do this step manually and not rely on an online tutorial. Each dataset has its on intricacies that may not be captured by a fixed / standalone tutorial.

Answer 1

[andy.wang]

If I were you, I would also do it manually. Things have changed dramatically on file structures. Previous version of script may not be pertinent to your data set.

You can just download the RsMergeArch.vcf.gz from dbSNP ftp server. It records all rs numbers merging history until build 151. Extract the first column, sort it and use the "comm" command to compare to your own data. With this, you can see what snps in your data has been changed.