Question: Error in GWAS using GenABEL package
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gravatar for jaafari.omid
5 months ago by
jaafari.omid50
jaafari.omid50 wrote:

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 recognised !

Your help and suggestion is appreciated in advance.

Kind regards, Omid

gwas snp next-gen R genome • 186 views
ADD COMMENTlink written 5 months ago by jaafari.omid50
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