Question: Beagle VCF header issue
0
gravatar for vmuir
6 months ago by
vmuir0
vmuir0 wrote:

I've received a bed/bim/fam set of data that I'm trying to use for imputation, and I'm having issues with the VCF header going into beagle.

I can shift things over into VCF format with plink2 (with or without filtering out MAF = 0 alleles, since that can maybe be an issue with Beagle4.1) without a hitch.

plink2 --bfile data --recode vcf --out data_vcf

However, when I try to run the following beagle command

java -Xss5m -Xmx10g -jar beagle.27Jan18.7e1.jar gt=data_vcf.vcf ref=chr17.1kg.phase3.v5a.b37.bref3 out=imputed_chr17 chrom=17 impute=true

I get this error:

Exception in thread "main" java.lang.IllegalArgumentException: Missing line (#CHROM ...) after meta-information lines

Calling the head of the VCF gives me this:

##fileformat=VCFv4.3
##fileDate=20181024
##source=PLINKv2.00
##contig=<ID=1,length=249210708>
##contig=<ID=2,length=243020724>
##contig=<ID=3,length=197587302>
##contig=<ID=4,length=190743787>
##contig=<ID=5,length=180580060>
##contig=<ID=6,length=170882051>
##contig=<ID=7,length=159018205>
##contig=<ID=8,length=146293415>
##contig=<ID=9,length=141031899>
##contig=<ID=10,length=135190430>
##contig=<ID=11,length=134763142>
##contig=<ID=12,length=133718411>
##contig=<ID=13,length=115087914>
##contig=<ID=14,length=107225162>
##contig=<ID=15,length=102376656>
##contig=<ID=16,length=90138741>
##contig=<ID=17,length=81041078>
##contig=<ID=18,length=78014321>
##contig=<ID=19,length=58864480>
##contig=<ID=20,length=62852399>
##contig=<ID=21,length=48015687>
##contig=<ID=22,length=51156667>
##contig=<ID=X,length=155236713>
##contig=<ID=Y,length=28802548>
##INFO=<ID=PR,Number=0,Type=Flag,Description="Provisional reference allele, may not be based on real reference genome">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT ...

The #CHROM line seems to be there. Any ideas as to what might be going on or how I can fix it?

beagle snp imputation • 348 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by vmuir0
0
gravatar for vmuir
6 months ago by
vmuir0
vmuir0 wrote:

And just solved my own question...

If anyone else has run into this. The issue is with the reference. I should have been calling

ref=chr17.1kg.phase3.v5a.vcf.gz
ADD COMMENTlink written 6 months ago by vmuir0
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