Clara Parabricks
v3.7
What's New?
New Tools
annotatebamwithumis
bamsort
consensusreads
groupreadsbyumi
setmateinfo
deeptrio
kallisto
muse
prepon
postpon
snpswift
votebasedvcfmerger
Improvements
General
Germline/Somatic
RNA
Bug Fixes
Germline/Somatic
RNA
CollectMultipleMetrics
Getting Started with Clara Parabricks
Installation Requirements
Hardware Requirements
Software Requirements
Verifying Hardware and Software Requirements
Checking available Nvidia hardware and driver
Checking available CPU RAM and threads
Checking nvidia-docker2 installation
Checking python version
Licensing
Distribution Options
Getting the Software
Installing the Software
Node Locked License, Docker Container
Prerequisites
Software Installation
Node Locked License, Singularity Container
Prerequisites
Software Installation
Node Locked License, Debian Package Installation
Prerequisites
Software Installation
Install Anaconda
Create and activate a basic environment
Create environments for extra tools
Flexera License, Docker Container
Prerequisites
License Installation
Software Installation
Flexera License, Singularity Container
Prerequisites
License Installation
Software Installation
Flexera License, Debian Package
Prerequisites
License Installation
Software Installation
Install Anaconda
Create and activate a basic environment
Create environments for extra tools
Additional Installation Options
Performance Tuning
Use a Fast SSD
DGX Users
Specifying which GPUs to use
Uninstalling the software
Software Overview
Software Tools
Pipelines
Compatible CPU Software Versions
Tutorials
Getting The Sample Data
FQ2BAM Tutorial
HaplotypeCaller
VCF QC By Bam
How-Tos
Whole-Genome Variant Calling
Software Requirements
Hardware Requirements
Introduction
Example data
Downloading and Indexing a Reference Genome and Known Sites
Aligning Reads
Generating a Comprehensive Set of Variant Calls with DeepVariant, HaplotypeCaller, and Strelka
Intermediate Quality Control with vcfqc
Merging Variant Callsets from Multiple Callers into one VCF File
Annotating Variant Calls with Information from Databases
Whole-Genome Somatic Small Variant Calling
Software Prerequisites
Compute Requirements and Configuration
Introduction
Download Example FASTQ Files
Downloading and Indexing a Reference Genome and Known Sites
Index Reference Genome
Step1: Aligning the Fastq Files to the Reference Genome
Step2: Generating a Set of Small Variant Calls Using Clara Parabricks Mutect2
Step3: For Validating the SNV and MNV Variants with truth set
Use GATK4 FilterMutectCalls to Apply Filters to the Raw Output of Mutect2
Intermediate Quality Control with vcfqc
Merging Variant Callsets from Multiple Callers into One VCF File
Annotating Variant Calls with Information from Databases
References and Useful Links
Technical Reference
Tools By Category
FASTQ and BAM Processing
applybqsr
bam2fq
bqsr
fq2bam
Variant Callers
bcftoolscall
cnvkit
deepvariant
haplotypecaller
lofreq
manta
muse
mutectcaller
smoove
somaticsniper
somaticsniper_workflow
strelka
strelka_workflow
RNA
RNA FQ2BAM (STAR)
starfusion
QC and BAM Analysis
bammetrics
bcftoolsmpileup
collectmultiplemetrics
samtoolsmpileup
splitncigar
Variant Processing
cnnscorevariants
dbsnp
frequencyfiltration
variantfiltration
vcfanno
vcfqc
vcfqcbybam
votebasedvcfmerger
vqsr
UMI Processing
umi_fgbio
annotatebamwithumis
bamsort
consensusreads
groupreadsbyumi
setmateinfo
Joint Calling
triocombinegvcf
glnexus
GVCF Processing
indexgvcf
genotypegvcf
Alphabetical list of all tools
annotatebamwithumis
Quick Start
annotatebamwithumis Reference
applybqsr
Quick Start
Compatible GATK4 Command
applybqsr Reference
arriba
Quick Start
arriba Reference
bam2fq
Quick Start
Compatible CPU-based BWA-MEM, GATK4 Commands
bam2fq Reference
bammetrics
Quick Start
Compatible GATK4 Command
bammetrics Reference
bamsort
Quick Start
bamsort Reference
bcftoolscall
Quick Start
Compatible CPU Command
bcftoolscall Reference
bcftoolsmpileup
Quick Start
Compatible BCFTools Command
bcftoolsmpileup Reference
bqsr
Quick Start
Compatible GATK4 Command
bqsr Reference
cnnscorevariants
Quick Start
Compatible GATK4 Command
Post-analysis Filtering
cnnscorevariants Reference
cnvkit
Quick Start
cnvkit Reference
collectmultiplemetrics
Quick Start
Compatible GATK4 Command
collectmultiplemetrics Reference
consensusreads
Quick Start
consensusreads Reference
dbsnp
Quick Start
dbsnp Reference
deeptrio
Quick Start
Compatible Google DeepVariant Commands
deeptrio Reference
deepvariant
Quick Start
Compatible Google DeepVariant Commands
deepvariant Reference
deepvariant_germline
Quick Start
deepvariant_germline Reference
demuxfastqs
Quick Start
demuxfastqs Reference
denovomutation
Quick Start
denovomutation Reference
expansionhunter
Quick start
expansionhunter Reference
fq2bam
Quick Start
Compatible CPU-based BWA-MEM, GATK4 Commands
fq2bam Reference
frequencyfiltration
Quick Start
frequencyfiltration Reference
genotypegvcf
Quick Start
Compatible CPU GATK4 Command
genotypegvcf Reference
germline
Quick Start
DNAnexus
Compatible CPU-based BWA-MEM, GATK4 Commands
germline Reference
glnexus
Quick Start
glnexus Reference
groupreadsbyumi
Quick Start
groupreadsbyumi Reference
haplotypecaller
Quick Start
Compatible GATK4 Command
haplotypecaller Reference
human_par
Quick Start
Compatible CPU-based BWA-MEM, GATK4 Commands
human_par Reference
indexgvcf
Quick Start
Compatible CPU GATK4 Command
indexgvcf Reference
kallisto
Quick Start
kallisto Reference
lofreq
Quick Start
Compatible CPU Command
lofreq Reference
manta
Quick Start
manta Reference
muse
Quick Start
Compatible CPU Command
muse Reference
mutectcaller
Quick Start
Compatible GATK4 Command
Mutect2 with Panel of Normals
mutectcaller Reference
postpon
Quick Start
postpon Reference
prepon
Quick Start
prepon Reference
rna_fq2bam
Quick Start
Compatible CPU Command
rna_fq2bam Reference
rna_gatk
Quick Start
rna_gatk Reference
samtoolsmpileup
Quick Start
Compatible SAMTools Command
samtoolsmpileup Reference
setmateinfo
Quick Start
setmateinfo Reference
smoove
Quick Start
Compatible CPU Command
smoove Reference
snpswift
Quick Start
snpswift Reference
somatic
Quick Start
somatic Reference
somaticsniper
Quick Start
Compatible CPU Command
somaticsniper Reference
somaticsniper_workflow
Quick Start
Compatible CPU Command
somaticsniper_workflow Reference
splitncigar
Quick Start
Compatible GATK Command
splitncigar Reference
starfusion
Quick Start
Compatible CPU Command
starfusion Reference
strelka
Quick Start
strelka Reference
strelka_workflow
Quick Start
Compatible GATK4 Command
strelka_workflow Reference
triocombinegvcf
Quick Start
Compatible CPU GATK4 Command
triocombinegvcf Reference
umi_fgbio
Quick Start
umi_fgbio Reference
variantfiltration
Quick Start
Compatible GATK4 Command
variantfiltration Reference
vcfanno
Quick Start
vcfanno Reference
vcfqc
Quick Start
vcfqc Reference
vcfqcbybam
Quick Start
vcfqcbybam Reference
votebasedvcfmerger
Quick Start
votebasedvcfmerger Reference
vqsr
Quick Start
Compatible GATK4 Command
vqsr Reference
Comparison with Baseline Tools
BAM Comparison
BQSR Report Comparison
VCF Comparison
Publications
Academic References to Clara Parabricks
See Also
Frequently asked questions
Why isn't my license working?
How do I ensure that my Parabricks analysis won't terminate if I lose my SSH connection?
Parabricks does not run when a system is initialized when using Singularity containerization
User Forum
Third Party Software Notices
BWA
GATK
DEEPVARIANT
HTSLIB
SAMTOOLS
BCFTOOLS
CNVKIT
SOMATICSNIPER
STAR
STAR-FUSION
TCMALLOC
GLNEXUS
STRELKA
MANTA
SMOOVE
MUSE
ISA-L
LOFREQ
VCFANNO
Clara Parabricks
Docs
»
Technical Reference
»
Tools By Category
»
Joint Calling
Joint Calling
ΒΆ
NVIDIA Clara Parabricks Pipelines accelerated tools for joint calling.
triocombinegvcf
glnexus