beagle error: genotype is missing allele separator

0

I am trying to impute a VCF table that was created by GATK and then filtered with VCFtools with beagle.
when I run the following code:

file=chr1.vcf java -Xmx144g -jar /home/pogoda/software/BEAGLE/beagle.03Jul19.b33.jar gt=${file} nthreads=36  out=IMPUTED_${file}

I get the following error: ERROR: genotype is missing allele separator:
couldn't find any information online, any suggestions?
thanks!


genomics


imputation


bioinformatics

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