I am trying to run the annotation for MAGMA using the Gene locations, build 37 and european populations.
When I run the following code:
magma --annotate window=20,20 --snp-loc NCBI37.3.gene.loc --gene-loc g1000_eur.bim --out build
It skips every line and gives the error:
WARNING: on line 5522658, chromosome code 'rs188565905' not recognised; skipping gene (ID = 4)
at every position.
Also only a log file is produced. All of my files are in the same directory and they were taken from the magma site. Any information on where the issue lies?