Off topic:gtool conversion error

Question

[jkatz77]

I am trying to convert a .gen file to a .map and a .ped file using gtool. The problem is, despite having 498 SNPs in my Gen file, the map file being created only has the first snp and is only 1 row long. The command I am using is:

gtool -G --g GENE.gen \
--s SAMPLE.sample \
--ped PED.ped \
--map MAP.map \
--phenotype phenotype --sex sex \
--num_snps 498 \
--num_samples 966 \
--chr 11 \
--snp \
--log SORL1.log