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GATK haplotypeCaller output MQ in vcf for non variant sites

Hi I am using following command to run gatk haplotypeCaller

        {params.gatk_path} {params.gatk_params} HaplotypeCaller \
            -R ${{ref}} \
            -I {input.bam} \
            -O {output.gvcf} \
            -ERC GVCF \
            -G StandardAnnotation \
            -G AS_StandardAnnotation \
            -L {params.chr_num} \
            --native-pair-hmm-threads {threads} \
            --output-mode EMIT_ALL_ACTIVE_SITES

I expected the following:

  • output all callable site even if they are homozygous as ref
  • output (RMS) MQ, DP for all site outputed

I find that point 1 is ok, but the gvcf file miss MQ for sites homozygous as ref (non variant sites).

Can I update some params to fix this question?

vcf mq gatk ngs
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written by octpus616 • octpus616

1 answer 

    -ERC GVCF

you're calling in GVCF mode. Using this GVCF is useless until you call gatk GenotypeGVCFs

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

yeah I have apply GenotypeGVCFs in next step, but GenotypeGVCFs cant output vcf with MQ because gvcf dont have this fields for non variant sites

• 0 views • link
written by octpus616 • octpus616

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