GATK haplotypeCaller output MQ in vcf for non variant sites

Question

[octpus616]

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?

Answer 1

[Pierre Lindenbaum]

    -ERC GVCF 

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

[octpus616]

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