Error in BeagleOutputToVCF

hirokomatsui

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

Geraldine_VdAuwera

Hi Hiroko,

This looks like a bug that was fixed in version 2.3. Could you please upgrade to the latest version and try again?

hirokomatsui

I see the same error with GATK version 2.3-6-gebbba25.

hirokomatsui

I don't know if it's related, but there's a SNP which my input VCF file says, chr1 10140662 rs75035497 C G

and my gprobs file has a report at the region: chr1:10140662 CT C

so does phased file say: M chr1:10140662 CT CT CT C CT

At this regions, GATK show an error message: MESSAGE: Allele in genotype CT not in the variant context [C*, G]

Thanks, Hiroko

Geraldine_VdAuwera

Hmm, maybe. Could you please upload a snippet of your files for testing? Instructions are here if needed:

http://www.broadinstitute.org/gatk/guide/article?id=1894

hirokomatsui

I have uploaded a file, hm.tar.gz, at ftp.broadinstitute.org. There are snippet of files, gprobs, phased, r2 and vcf in the tar ball, and the command line and the stack trace are in the file console.txt. Thanks for your help. Hiroko

hirokomatsui

Sorry that was my wrong, I had to remove the records from the VCF file, which I filtered out from beagle input file. Thank you for taking your time. Hiroko

NGCrawford

I'm getting the same error and "BeagleOutputToVCF" works correctly on all my chromosomes but one. Is there a way to get it the error message to emit the position of the offending SNV?

NGCrawford

Also, I'm running GenomeAnalysisTK-2.4-3-g2a7af43.

Geraldine_VdAuwera

@NGCrawford, you can append -l DEBUG to your command line to activate debug output. BTW that's lowercase L, not uppercase i.