Haplotypecaller producing an empty VCF file

Hello everyone,

I’m encountering an issue with GATK’s HaplotypeCaller while working with RNA-seq data using NVIDIA Parabricks. Despite following the recommended steps, the output VCF file is empty, indicating no variants were called.


  • Tool: GATK HaplotypeCaller via NVIDIA Parabricks
  • Data Type: RNA-seq
  • Reference Genome: Mus musculus (GRCm39)
  • BAM FILE: Was produced via NVIDIA Parabrick’s rna_fq2bam
docker run --rm --gpus all     -v /home/$USER:/workdir     nvcr.io/nvidia/clara/clara-parabricks:4.3.1-1     pbrun haplotypecaller     --ref /workdir/ref/Mus_musculus.GRCm39.dna.primary_assembly.fa     --in-bam /workdir/output/aligned_reads.bam     --out-variants /workdir/output/germline_variants.vcf --rna

I have checked the integrity of the BAM file with samtools as well as the contents and all seems to be okay.

Are there any pipeline’s available in parabricks similar to 3.8’s rna_gatk?