The following examples will require using the system console of the GPU host. Click on the “System Console” link in the left menu of this page to open a web-based SSH session.
HaplotypeCaller is the standard GATK variant caller. It takes as input the bam files produced earlier using the fq2bam tool. It assembles plausible haplotypes from active regions, and identifies genotype likelihoods according to Bayes’ Rule. The result is a Variant Call Format (VCF) file of all the variant calls across the genome, including their position in the genome and the allelic information.
docker run --gpus all --rm \
-v $(pwd):/results \
-v $(pwd):/data \
-w /data \
nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
pbrun haplotypecaller \
--ref ${REFERENCE_FILE} \
--in-bam /results/fastq2bam.pb.bam \
--out-variants /results/haplotype.vcf
You should have an output similar to the following :
[PB Info 2022-Sep-13 09:53:46] ------------------------------------------------------------------------------
[PB Info 2022-Sep-13 09:53:46] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2022-Sep-13 09:53:46] || Version 4.0.0-1 ||
[PB Info 2022-Sep-13 09:53:46] || GPU-GATK4 HaplotypeCaller ||
[PB Info 2022-Sep-13 09:53:46] ------------------------------------------------------------------------------
[PB Info 2022-Sep-13 09:54:01] 0 /results/fastq2bam.pb.bam/results/haplotype.vcf
[PB Info 2022-Sep-13 09:54:01] ProgressMeter - Current-Locus Elapsed-Minutes Regions-Processed Regions/Minute
[PB Info 2022-Sep-13 09:54:11] chr1:29707201 0.2 260635 1563810
[PB Info 2022-Sep-13 09:54:21] chr1:69537601 0.3 591677 1775031
[PB Info 2022-Sep-13 09:54:31] chr1:108724801 0.5 919847 1839694
[PB Info 2022-Sep-13 09:54:41] chr1:166252801 0.7 1237572 1856358
[PB Info 2022-Sep-13 09:54:51] chr1:203313601 0.8 1547183 1856619
…
[PB Info 2022-Sep-13 10:08:51] chrUn_KI270438v1:105601 14.8 24280359 1636878
[PB Info 2022-Sep-13 10:09:01] chrUn_KI270438v1:105601 15.0 24280359 1618690
[PB Info 2022-Sep-13 10:09:11] chrEBV:168001 15.2 24280359 1600902
[PB Info 2022-Sep-13 10:09:21] Total time taken: 920.399908
[PB Info 2022-Sep-13 10:09:21] ------------------------------------------------------------------------------
[PB Info 2022-Sep-13 10:09:21] || Program: GPU-GATK4 HaplotypeCaller ||
[PB Info 2022-Sep-13 10:09:21] || Version: 4.0.0-1 ||
[PB Info 2022-Sep-13 10:09:21] || Start Time: Tue Sep 13 09:53:46 2022 ||
[PB Info 2022-Sep-13 10:09:21] || End Time: Tue Sep 13 10:09:21 2022 ||
[PB Info 2022-Sep-13 10:09:21] || Total Time: 15 minutes 35 seconds ||
[PB Info 2022-Sep-13 10:09:21] ------------------------------------------------------------------------------
/usr/local/parabricks/binaries//bin/htvc /data/Test/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna /results/fastq2bam.pb.bam 4 -o /results/haplotype.vcf -nt 5
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation