DeepVariant is a DeepLearning CNN-based germline variant caller. Parabricks has accelerated DeepVariant to extensively use GPUs and can run 30x WGS analysis in 25 minutes instead of hours.
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.
DeepVariant can be run in the same way that we did for the previous tools using ParaBricks.
docker run --gpus all --rm \
-v $(pwd):/results \
-v $(pwd):/data \
-w /data \
nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1 \
pbrun deepvariant \
--ref ${REFERENCE_FILE} \
--in-bam /results/fastq2bam.pb.bam \
--out-variants /results/deepvariant.vcf
You should have an output similar to the following :
Detected 4 CUDA Capable device(s), considering 4 device(s)
CUDA Driver Version / Runtime Version 11.4 / 11.2
Using model for CUDA Capability Major/Minor version number: 75
[PB Info 2022-Sep-13 10:12:52] ------------------------------------------------------------------------------
[PB Info 2022-Sep-13 10:12:52] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2022-Sep-13 10:12:52] || Version 4.0.0-1 ||
[PB Info 2022-Sep-13 10:12:52] || deepvariant ||
[PB Info 2022-Sep-13 10:12:52] ------------------------------------------------------------------------------
[PB Info 2022-Sep-13 10:12:52] Starting DeepVariant
[PB Info 2022-Sep-13 10:12:52] Running with 4 gpu, each with 4 workers
[PB Info 2022-Sep-13 10:13:04] ProgressMeter - Current-Locus Elapsed-Minutes
[PB Info 2022-Sep-13 10:13:10] ProgressMeter - chr1:10000 0.1
[PB Info 2022-Sep-13 10:13:16] ProgressMeter - chr1:10000 0.2
…
[PB Info 2022-Sep-13 11:01:34] ProgressMeter - chr22:46924000 48.5
[PB Info 2022-Sep-13 11:01:40] ProgressMeter - chr22:49884000 48.6
[PB Info 2022-Sep-13 11:01:46] ProgressMeter - chrX:3415000 48.7
…
[PB Info 2022-Sep-13 11:06:10] ProgressMeter - chrY:17408000 53.1
[PB Info 2022-Sep-13 11:06:19] Deepvariant is finished, total time is 3194.386 seconds
[PB Info 2022-Sep-13 11:06:19] ------------------------------------------------------------------------------
[PB Info 2022-Sep-13 11:06:19] || Program: deepvariant ||
[PB Info 2022-Sep-13 11:06:19] || Version: 4.0.0-1 ||
[PB Info 2022-Sep-13 11:06:19] || Start Time: Tue Sep 13 10:12:52 2022 ||
[PB Info 2022-Sep-13 11:06:19] || End Time: Tue Sep 13 11:06:19 2022 ||
[PB Info 2022-Sep-13 11:06:19] || Total Time: 53 minutes 27 seconds ||
[PB Info 2022-Sep-13 11:06:19] ------------------------------------------------------------------------------
/usr/local/parabricks/binaries//bin/deepvariant /data/Test/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna /results/fastq2bam.pb.bam 4 -o /results/deepvariant.vcf --model /usr/local/parabricks/binaries//model/75/shortread/deepvariant.eng -n 4 --channel_insert_size --pileup_image_width 221 --max_reads_per_partition 1500 --partition_size 1000 --vsc_min_count_snps 2 --vsc_min_count_indels 2 --vsc_min_fraction_snps 0.12 --min_mapping_quality 5 --min_base_quality 10 --alt_aligned_pileup none --variant_caller VERY_SENSITIVE_CALLER
Please visit https://docs.nvidia.com/clara/#parabricks for detailed documentation