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GenotypeGVCFs

lawallawal United KingdomMember

I was trying to do combine sets of vcf files for all my samples so that I have one single vcf output using this command option below
java -d64 -Xmx48g -jar ${GATK}/GenomeAnalysisTK.jar \
-R ${REF} \
-T GenotypeGVCFs \
--variant A.g.vcf \
--variant B.g.vcf \
--variant C.g.vcf \
-stand_emit_conf 30 \
-stand_call_conf 30 \
-o genotype.vcf

but I got this error message
“The following invalid GT allele index was encountered in the file: END=21994810”. I have tried to locate where the problem could be coming from but I do not understand this. Could you please advise me.

Best Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    Accepted Answer

    @lawal
    Hi,

    So, the line you posted is from the re-generated GVCF? The issue is that instead of the GT field, there is an END position.

    Did you restart the Haplotype Caller from the beginning when you ran out of disk space? Can you confirm you are using the latest version of GATK? You may just need to run Haplotype Caller on sample A again to get a clean GVCF.

    Thanks,
    Sheila

Answers

  • lawallawal United KingdomMember

    Thank you Tommy. I found this in A.g.vcf only. I remember I ran out of disk space along the line but I had to create more space later and re-generated the A.g.vcf.

    1 21991582 . T . . END=21991582 GT:. END=21994810 GT:DP:GQ:MIN_DP:PL 0/0:36:96:35:0,96,1440

  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    Accepted Answer

    @lawal
    Hi,

    So, the line you posted is from the re-generated GVCF? The issue is that instead of the GT field, there is an END position.

    Did you restart the Haplotype Caller from the beginning when you ran out of disk space? Can you confirm you are using the latest version of GATK? You may just need to run Haplotype Caller on sample A again to get a clean GVCF.

    Thanks,
    Sheila

  • lawallawal United KingdomMember

    @Sheila yes i am using the latest GATK version and I did restart the Haplotype Caller from the beginning. @Geraldine_VdAuwera, thank you and I will just redo the job as advised to get clean job.

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