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