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Henri-Jean Garchon

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    Henri-Jean Garchon commented,

    1. Community
    2. Germline
    3. GenotypeGVCFs : VariantQueryProcessorException

    Hi Genevieve, I forgot to address the first question you raised in your comment. The GVCF were not concatenated. I am not sure of which bedfile you are referring to. Best regards Henri-Jean

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    Henri-Jean Garchon commented,

    1. Community
    2. Germline
    3. GenotypeGVCFs : VariantQueryProcessorException

    Hi Genevieve, I apologize for my late reply. I just uploaded the vidmap.json at the indicated ftp site. The filename is "GenotypeGVCFs_VQPE_vidmap.json". Best regards Henri-Jean

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    Henri-Jean Garchon commented,

    1. Community
    2. Germline
    3. GenotypeGVCFs : VariantQueryProcessorException

    Hi Genevieve, Thank you for feedback. Here is the HaplotypeCaller command, retrieved from the header of the sample VCF file : ##GATKCommandLine=<ID=HaplotypeCaller,CommandLine="HaplotypeCaller --st...

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    Henri-Jean Garchon created a post,

    GenotypeGVCFs : VariantQueryProcessorException

    1. Community
    2. Germline

    REQUIRED for all errors and issues: a) GATK version used: 4.3.0.0 Java runtime: OpenJDK 64-Bit Server VM v11.0.16+8-post-Debian-1deb11u1 b) Exact command used:  /usr/local/bin/gatk-4.3.0.0/gatk --j...

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