Version v0.1.1

• Upgrade to Parabricks v4.3.0.1
• Specify the number of GPUs for each Parabricks process
• Specify GPU devices by device-id in Docker conf

Version 0.1.0

GPU and CPU NGS analysis and QC pipelines

GPU germline-pipeline using NVIDIA Parabricks

• fq2bam
• applybqsr
• haplotypecaller
• deepvariant

CPU germline-pipeline using

• BWA MEM & SAMTools sort
• GATK MarkDuplicates
• GATK BaseRecalibrator
• GATK ApplyBQSR
• GATK HaplotypeCaller

QC pipeline (CPU-only)

• FASTQC
• SAMtools flagstat
• SAMtools stat
• Mosdepth
• GATK CollectInsertSizeMetrics
• GATK collectAlignmentSummaryMetrics
• MultiQC