Question: Error while running BEAGLE for genotype imputation
gravatar for Shab86
4.7 years ago by
Shab86270 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 • 2.9k views
ADD COMMENTlink modified 2.6 years ago by prakashgenetics0 • written 4.7 years ago by Shab86270

please help me im getting this error while running beagle imputation

Exeption in thread main java.lang.OutOfMemmoryError:java heap space 
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ADD REPLYlink modified 2.6 years ago by lakhujanivijay5.3k • written 2.6 years ago by prakashgenetics0

Please use proper markup to format the text. I have done it for you!

ADD REPLYlink written 2.6 years ago by lakhujanivijay5.3k

Here is my solution: remove non A, T, C, G variants:

plink --bfile RA2020-B8 --list-duplicate-vars ids-only suppress-first
plink --bfile RA2020-B8 --alleleACGT --snps-only just-acgt --exclude plink.dupvar --make-bed --out RA2020-B9
ADD REPLYlink modified 11 months ago • written 11 months ago by Shicheng Guo8.5k
gravatar for WouterDeCoster
4.7 years ago by
WouterDeCoster45k 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:

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 4.7 years ago by WouterDeCoster45k

Awesome ! Thanks for your answer :)

ADD REPLYlink written 4.7 years ago by Shab86270

hello, i have the same problem that there are '-' at alt column of my vcf file, how can i prefilter it. thanks, vinay

ADD REPLYlink written 2.5 years ago by vinayreddynannuru20
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