Open saurabhbelsare opened 2 years ago
Hi, I hope you are doing well. I have the same problem. I wanted to create phenotypes for sim1000g simulated genotypes.
@mahdikafi can you try the following.
configs/genotype.yaml
, change memory_cautious
to False and repeat pip installation of gepsi (pip install .
)
Hi, I'm trying to run a toy example with GEPSi, but am running into an error at the first step, to convert my genotypes to h5 format the way GEPSi expects. Here is my toy vcf generated from an msprime simulation:
I converted this vcf to .raw and .bim files using both, plink1.9 and plink2 with these commands:
I try to convert this to the h5/matrix_header format using the following command:
gepsi genotype --data_path ./ --matrix_name output.raw --snplist_name output.bim --ignore_gene_map --features "NONE" --annotation_name NONE
However, I'm getting errors at this step. They are different errors for plink1.9 and plink2. The error while trying to convert raw/bim files generated from plink1.9 is
and the error while trying to convert raw/bim files generated from plink2 is:
Which version of plink should I use, and how should I fix the corresponding error to get the h5/matrix_header files?
Thank you!