Question: Lift over based on physical position from GRCh37 build 137 to GRCh37 build 132
0
gravatar for Mr Locuace
3.2 years ago by
Mr Locuace90
Chile
Mr Locuace90 wrote:

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 !!

ADD COMMENTlink modified 3.2 years ago by Jeremy Leipzig18k • written 3.2 years ago by Mr Locuace90

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

ADD REPLYlink written 3.2 years ago by robm9119150

thank you for your help robm9119

ADD REPLYlink modified 3.2 years ago • written 3.2 years ago by Mr Locuace90
2
gravatar for Jeremy Leipzig
3.2 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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

 

ADD COMMENTlink written 3.2 years ago by Jeremy Leipzig18k
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