Beagle 4.1: Imputation - Error - ERROR: invalid ALT allele
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3.0 years ago

Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.51-1 (2017-09-28) x86_64 GNU/Linux,
beagle.27Jan18.7e1.jar, Version 4.1
Plink v1.90b4.9
VCF: fileformat=VCFv4.2
Map file: http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/ GRch37 version

I created VCF file using plink from .ped and .map file as input.

plink --file merlin_CHR22 --recode-vcf --out vcf_22

I run into an error while performing imputation for CHR22, ona small region of 5MB, as:

java -Xmx1000m -jar beagle.27Jan18.7e1.jar gt=vcf_22.vcf out=test ref=chr22.haplotypes.vcf.gz map=plink.chr22.GRCh37.map chrom=22:0-500000

Error:

Start time: 05:40 PM EDT on 04 Apr 2018
Command line: java -Xmx889m -jar beagle.jar
  gt=vcf_22.vcf
  out=test
  ref=chr22.haplotypes.vcf.gz
  map=plink.chr22.GRCh37.map
  chrom=22:0-500000
ERROR: invalid ALT allele at 22:17 [X]
ERROR: invalid ALT allele at 22:17 [X]

Any suggestions/ideas to fix this?

Thanks!

snp imputation • 1.6k views
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Have you tried BEAGLE 4.0 to see if you get the same error? Might be worth a shot. I had a similar error - sorry, can't remember it exactly, and I was able to use BEAGLE 4.0 without the error.

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