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GenomicsDBImport update database and MQ values

Dear GATK Team,

I recently stumbled upon a problem, maybe you can help with that! I've recently done a multisample calling (around 1000 genomes) using the new GenomicsDBImport and then GenotypeGVCFs on it.
Since in the latest versions of GATK you implemented the possibility of adding one or more samples to the DB and I needed to do it, I gave it a try updating the old (successful) DB and recalling with GenotypeGVCFs. See simplified command line below:

$GATK --java-options "-Xmx42G"  GenomicsDBImport --reader-threads 6 \
        --genomicsdb-update-workspace-path ${CHUNKDBDIR} \
        --sample-name-map ${SAMPLEMAP}   \
        --intervals ${BED_PATH}/${BEDID}.bed \
        --batch-size 500 \
        2> ${CHUNKLOG}

    $GATK --java-options "-Xmx42G" GenotypeGVCFs \
        -V gendb://${CHUNKDBDIR} \
        -R ${REF} \
        -O ${VCF} \
        2> ${VCFLOG}

Batch size and chunking of the genomes, obviously were identical.
The problem is that the resulting dataset after GenotypeGVCFs was missing MQ values. Did I do anything wrong?
All the scripts ended with no error.

Thanks for your attention and help!
Best

Riccardo

Answers

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