Use genotypegvcf with GenomicsDB workspace

Hello!

Im trying to perform joint genotyping on one or more samples pre-called with HaplotypeCaller using gatk genotypegvcf (https://gatk.broadinstitute.org/hc/en-us/articles/360046224151-GenotypeGVCFs).

I have created GenomicsDB workspace with GenomicsDBImport, but it looks that pbrun genotypegvcf doesn’t work when GenomicsDB.

I am able to converts variant calls in g.vcf format to VCF, but why does GenomicsDB doesn’t work?

Command I’m using:

singularity run \
    --nv \
    ${PARABRICKS_DIR}/clara-parabricks_4.0.0-1.sif \
    pbrun genotypegvcf \
    --ref $HG19FASTAPATH \
    --in-gvcf gendb://${DBPATH}/gatk.database_vanagi_ALL \
    --out-vcf ${OUTPATH}/database_vanagi_ALL.output.vcf.gz
    --num-gpus 2 \

Output:

[Parabricks Options Error]: Input file gendb:///home_beegfs/edgars01/Ineta/WGS/gatk.database_vanagi_ALL not found.
Exiting...
[Parabricks Options Error]: Run with -h to see help

genotypegvcf doesn’t recognize GenomicsDB

Hi,

We are sorry but the input --in-gvcf should be a g.vcf or g.vcf.gz file, and not a GenomicsDB workspace.

Best,
Myrieme

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