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I'm having a problem running BeagleOutputToVCF, showing an error message:

##### ERROR stack trace
java.lang.IllegalStateException: Allele in genotype AT not in the variant context [A*, G]
        at org.broadinstitute.sting.utils.variantcontext.VariantContext.validateGenotypes(VariantContext.java:1197)
        at org.broadinstitute.sting.utils.variantcontext.VariantContext.validate(VariantContext.java:1137)
...

Is this because my Beagle output file include INDELs?

I'm using GenomeAnalysisTK-2.2-10-gbbafb72, and the command line is like:

> java -Xmx4g -jar /raid/software/src/GenomeAnalysisTK-2.3-5-g49ed93c/GenomeAnalysisTK.jar \
-R hg19_lite.fa \
-T BeagleOutputToVCF \
-V chr1.01.vcf \
-beagleR2:BEAGLE beagle/chr1.01.r2 \
-beaglePhased:BEAGLE chr1.01.phased \
-beagleProbs:BEAGLE chr1.01.gprobs \
-o beagle_vcf/chr1.01.vcf \
-L 1:1-10000000

Thanks, Hiroko Matsui

There are 9 comments on this article. To see them or add your own, read this post on the forum