No software to combine .gvcf files in 4.0

It’s a very important step to combine multiple samples’ gvcf files together in the pipeline of joint calling.
In GATK, it could be done with CombineGVCFs.
But in Parabricks 4.0, I can’t find the corresponding software.
And in previous version, some join calling functions has been implemented, such as CombineGVCFs (but can only input 2 or 3 gvcfs) and GLNexus.

So is there any future plan to add the function back and free the limitation of the number of gvcf files?

Do you mean this tool genotypegvcf? @minerw1024

Thanks for your reply.

But it’s a pity that I cannot use that in the joint calling for multiple gvcf files.

I tried genotypegvcf in followed code:

docker run \
        --gpus all \
        --rm \
        --volume $(pwd):/workdir \
        --volume $(pwd):/outputdir \
        nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
        pbrun genotypegvcf \
        --ref /workdir/refs/refdata.fna \
        --in-gvcf /workdir/gvcf/0010.g.vcf \
        --in-gvcf /workdir/gvcf/0011.g.vcf \
        --in-gvcf /workdir/gvcf/0012.g.vcf \
        --in-gvcf /workdir/gvcf/0013.g.vcf \
        --in-gvcf /workdir/gvcf/0014.g.vcf \
        --in-gvcf /workdir/gvcf/0015.g.vcf \
        --in-gvcf /workdir/gvcf/0016.g.vcf \
        --in-gvcf /workdir/gvcf/0017.g.vcf \
        --in-gvcf /workdir/gvcf/0018.g.vcf \
        --in-gvcf /workdir/gvcf/0019.g.vcf \
        --out-vcf /outputdir/001x.vcf

It throws no error. But after it’s finished, I used bcftools to check the result file, the outputs shows only the last gvcf file is converted:

$ bcftools query -l 001x.vcf
0019

So what is the right command to use it ?

I’m not sure, but you may try to use this option --in-selectvariants-dir just to specify the gvcf files directory(e.g. /workdir/gvcf/).