Question: Error while running BEAGLE for genotype imputation
0
gravatar for Shab86
2.2 years 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 • 1.2k views
ADD COMMENTlink modified 16 days ago by prakashgenetics0 • written 2.2 years ago by Shab86220
3
gravatar for WouterDeCoster
2.2 years ago by
Belgium
WouterDeCoster29k 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 2.2 years ago by WouterDeCoster29k

Awesome ! Thanks for your answer :)

ADD REPLYlink written 2.2 years ago by Shab86220
0
gravatar for prakashgenetics
16 days ago by
prakashgenetics0 wrote:
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)
ADD COMMENTlink modified 16 days ago by Vijay Lakhujani2.5k • written 16 days ago by prakashgenetics0
0
gravatar for prakashgenetics
16 days ago by
prakashgenetics0 wrote:

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)
ADD COMMENTlink modified 16 days ago by Vijay Lakhujani2.5k • written 16 days ago by prakashgenetics0

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

ADD REPLYlink written 16 days ago by Vijay Lakhujani2.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 682 users visited in the last hour