Lift over based on physical position from GRCh37 build 137 to GRCh37 build 132

Question

[Mr Locuace]

Hello, I have 2 files, A and B, with human genome SNP data (630000 SNPs). Both are GRCh37 but A is build 137 and B is build 132. A has rs numbers and physical positions and B has physical positions and ancestral allele info, but no rs numbers. I want to lift over physical positions from build 137 to build 132 in order to get ancestral alleles (B) for rs numbers in A.

The best tool I have found so far is the UCSC Genome Bioinformatics server, but unfortunately it does convert only e.g. from GRCh37 to GRCh38, but not between builds from GRCh37.

Other questions from Biostars have address related topics but not intra-GRCh37 lift over.

I also tried liftOver package but it does not work for my case and I only found some poor documentation.

Any suggestion will be welcome!

[robm9119]

I am not sure if UCSC provides "chain file" to map within the same genome build. Here is a tutorial I found very easy to follow for using liftOver at the command line:

http://www.geneticlegacies.com/2012/01/basic-guide-to-ucsc-liftover-command.html

[Mr Locuace]

thank you for your help robm9119

Answer 1

[Jeremy Leipzig]

A freeze is a freeze. Why would the physical positions change within a freeze for any SNP on the primary assembly?

A: Applying Patches To Grch Assembly