Mapping Fst Values To A Manhattan Plot By Rs#
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?
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confusedious
2 answers
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 .
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Pierre Lindenbaum
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.
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confusedious
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