FINEMAP - output files

Question

[khn]

Hello,

Is anybody familiar with FINEMAP? There are some output files but it is a little complicated to interpret and be used for further analysis.

I want to draw locus zoom, using the output files from the FINEMAP.

One of the output files is SNP file, which includes the data of log 10 bays and position. Also the tool creates LD file, so can I use those for locus zoom?

Answer 1

[christian.benner]

Hi,

You could input into locuszoom your metal formatted file with two columns ‘marker’ and ‘pvalue’ where you put the values in the ‘prob’ column from FINEMAP’s .snp file in the ‘pvalue’ column. You could also provide the values in the .ld file to locuszoom by parsing it to the accepted format.

Christian