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The -allSites option in GenotypeGVCFs did not emit every position

I was using the -allSites option in GenotypeGVCFs with 100 samples. I found that many positions were missing in the combined gvcf even though these positions have well-supported reference call in every individual gvcf files. I am using GATK 3.6-0. I wonder if there are some parameters I idid not use correctly. Thank you in advance.


  • SheilaSheila Broad InstituteMember, Broadie, Moderator
    edited October 2016


    Can you please post some example GVCF records that do not show up in the final VCF? Please also post the corresponding sections from the final VCF that show the missing positions.


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