Question: Error while running BEAGLE for genotype imputation
0
gravatar for Shab86
19 months ago by
Shab86220
Helsinki
Shab86220 wrote:

I am trying to run BEAGLE 4.1 for an imputation run. I have core exome chip data on variants of 20th chromosome in BED/BIM/FAM format, which I phased and converted to vcf format. Also, the reference format is in vcf which was phased. All the phasing was done in SHAPEIT and converted using the convert option in it.

But, now when I try to run a BEAGLE imputation run by this: java -jar beagle.jar gt=test.vcf ref=chr20.vcf impute=TRUE

I get an error saying this- ERROR: REF field is not a sequence of A, C, T, G, or N characters at newrs11467497:126156 [D]

I am a newbie in this and can't understand what the error is about. Can anyone please help me out?

snp vcf genome software error • 803 views
ADD COMMENTlink modified 19 months ago by WouterDeCoster23k • written 19 months ago by Shab86220
2
gravatar for WouterDeCoster
19 months ago by
Belgium
WouterDeCoster23k wrote:

If I remember correctly (it has been a while I used beagle) it only operates on SNP polymorphisms. And indeed, the position (rs11467497) you run into a problem with is an indel: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=11467497

The error message also explains that: the reference field should contain either A, C, T, G or N. But for this case the reference is 'CAAA' or '-'.

I suggest to prefilter your vcf file to remove indel polymorphisms.

ADD COMMENTlink written 19 months ago by WouterDeCoster23k

Awesome ! Thanks for your answer :)

ADD REPLYlink written 19 months ago by Shab86220
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