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MAGMA Annotation error

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?

magma annotation error
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updated by h.mon h.mon • written by naomibreslin95 • naomibreslin95

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written by Ram Ram

1 answer

I have never run MAGMA, but just by reading you command-line, it appears to me you are swapping the arguments:

--snp-loc NCBI37.3.gene.loc

--gene-loc g1000_eur.bim

Shouldn't be the other way around?

--snp-loc g1000_eur.bim --gene-loc NCBI37.3.gene.loc

The error message indicates the same:

hromosome code 'rs188565905' not recognised

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written by h.mon h.mon

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