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CombineVariants error: Allele in genotype not in variant context ...

nchuangnchuang Member
edited July 2015 in Ask the GATK team

Hi guys,

I am trying to find private variants that are not shared with 1000G or dbSNP vcfs. I followed the video tutorial method of using CombineVariants to combine my 3 vcfs before SelectVariants for the unique set. However, running CombineVariants throws this error below. I believe this might be related to using VQSR in INDEL mode because when I tried this without calibrating for Indels I did not get this error.

INFO 17:35:28,751 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:35:28,754 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:
INFO 17:35:28,754 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 17:35:28,754 HelpFormatter - For support and documentation go to
INFO 17:35:28,759 HelpFormatter - Program Args: -T CombineVariants -R /local/projects-t3/1000G/hu
man_g1k_v37_decoy.fasta -V:GBR /local/projects-t3/1000G/gbr.tranche2.master.pass.vcf -V
:ATHENS /local/projects-t3/1000G/athens.tranche2.master.pass.vcf -V:DBSNP /local/projec
ts-t3/1000G/annovar/humandb/dbsnp142.vcf -V:1kG /local/projects-t3/1000G/gatk.resource/1k
G_phase3.snps.b37.vcf -o gbr.vs.athens.tranche2.dbsnp.1kG.combined.pass.vcf -nt 8
INFO 17:35:28,764 HelpFormatter - Executing on Linux 2.6.18-371.4.1.el5 amd64;
Java HotSpot(TM) 64-Bit Server VM 1.8.0_40-b26.
INFO 17:35:28,765 HelpFormatter - Date/Time: 2015/07/27 17:35:28
INFO 17:35:28,765 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:35:28,765 HelpFormatter - --------------------------------------------------------------------------------
INFO 17:35:29,759 GenomeAnalysisEngine - Strictness is SILENT
INFO 17:35:29,992 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 17:35:31,990 MicroScheduler - Running the GATK in parallel mode with 8 total threads, 1 CPU thread(s) for each of 8 data thread(s), of 64 processors available on this machine
INFO 17:35:32,075 GenomeAnalysisEngine - Preparing for traversal
INFO 17:35:32,080 GenomeAnalysisEngine - Done preparing for traversal
INFO 17:35:32,081 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 17:35:32,082 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 17:36:04,522 ProgressMeter - 1:18016781 2792752.0 32.0 s 11.0 s 0.6% 92.9 m 92.3 m
INFO 17:36:10,985 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalStateException: Allele in genotype <:DEL> not in the variant context [AGAAG, AAGGAAG, A, AAGGA
at htsjdk.variant.variantcontext.VariantContext.validateGenotypes(
at htsjdk.variant.variantcontext.VariantContext.validate(
at htsjdk.variant.variantcontext.VariantContext.(
at htsjdk.variant.variantcontext.VariantContextBuilder.make(
at htsjdk.variant.variantcontext.VariantContextBuilder.make(
at org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils.simpleMerge(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(
at java.util.concurrent.ThreadPoolExecutor.runWorker(
at java.util.concurrent.ThreadPoolExecutor$

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.4-0-g7e26428):
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions
ERROR MESSAGE: Allele in genotype <:DEL> not in the variant context [AGAAG, AAGGAAG, A, AAGGA, AAGGAAGGAAGGA]
ERROR ------------------------------------------------------------------------------------------

Should be < *:DEL>


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