I am trying to run genome imputation, so i have my input file and then my phased reference.

I run the following code:

java -jar ${EBROOTBEAGLE}/beagle.jar gt=chr4.vcf.gz ref=Chr4_phased_snp.vcf.gz out=chr4_imputed 

And get the following error

ERROR: REF field is not a sequence of A, C, T, G, or N characters at 4:116707718 [D]

So I trouble shoot, I filter my vcf file so it is only SNPs (so no indels), also try to filter out any sites that do not have A,C,T,G, or N with the following code

bcftools view -i 'REF ~ "^[ACGTN]$"' input.vcf -o filtered_output.vcf

Run it again and get the same thing, so i say hmmm let me look at this specific site within my reference. Well, it does not exist. So just to be safe I run this to get rid of singletons

bcftools view -m2 -M2 -v snps -o output_no_missing.vcf -O v input.vcf.gz

Run beagle again and get the same error, so i say okay lets just use exclude sites with 4:116707718 because it is the problem child so i run

java -jar ${EBROOTBEAGLE}/beagle.jar gt=chr4.vcf.gz ref=Chr4_phased_snp.vcf.gz out=chr4_imputed excludemarkers=file.txt

Where the file has the marker site. I still get the same error. I am out of trouble shooting ideas... It took me forever to find a suitable reference, so I really can't afford to just go find a new one; plus, I am doing this by chromosome, and chromosomes 1-3 worked just fine.

Please help... Please :(