Hello dears all,
Actually I am running a plink data set (of a fish species) for GWAS using GenABEL package in R. The plink files have been generated from an imputed vcf file.
Here is the command that I used for imputation using Beagle:
java -Xms1000g -Xmx1000g -jar beagle.28Sep18.793.jar gt=snps_filtered-1.vcf.gz out=snps_filtered-1-1 imp-states=1600 nthreads=20
to convert the .vcf.gz file into the plink format I used the following command:
plink --vcf snps_filtered-1-1.vcf.gz --recode --out myplink-1 --allow-extra-chr --chr-set 22
Then when I want to run the plink files through GenABEL package in R, first it starts successfully to read the positions from map file and the genotypes using the ped file, but after that I get face with an error which says:
Read information for 272 people from file 'myplink-1.ped' Analysing
marker information ... Error in convert.snp.ped("myplink-1.ped",
"myplink-1.map", "Tilapia-1.genabel") : coding 'mo' for SNP not
Your help and suggestion is appreciated in advance.