Mapping Fst Values To A Manhattan Plot By Rs#

Question

[confusedious]

Hello everyone,

I have genome-wide pairwise Fst values for ~1 million SNPs and would like to put them onto a Manhattan plot.

My data files only contain the rs numbers (not bp position), so I will need to use a tool that can map these to a genome build.

Does anyone have any suggestions?

Answer 1

[Pierre Lindenbaum]

get the positions of the rs ( Get SNP position from a python interface. ) or use 'join'+ the data dump of the ucsc for snp137 before plotting .

Answer 2

[confusedious]

I have been informed that I should be able to do this without SNP positions via GoldenHelix. It has a function for mapping rs numbers to the build of preference as well as doing the plotting.