Error while running BEAGLE for genotype imputation

Question

[Shab86]

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?

[prakashgenetics]

please help me im getting this error while running beagle imputation

Exeption in thread main java.lang.OutOfMemmoryError:java heap space 
at phaser.ai.a(unkown sourse) 
at phaser.ai.a(unkown sourse) 
at phaser.ai.a(unkown sourse) 
at phaser.ai.a(unkown sourse)
at phaser.ai.a(unkown sourse)

[lakhujanivijay]

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

[Shicheng Guo]

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

Answer 1

[WouterDeCoster]

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.

[Shab86]

Awesome ! Thanks for your answer :)

[vinayreddynannuru]

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