clara/parabricks/3.7.0/Documentation/ToolDocs/StandaloneToolsOverview.html

NVIDIA Docs Hub NVIDIA Clara Clara Parabricks v3.7.0 clara/parabricks/3.7.0/Documentation/ToolDocs/StandaloneToolsOverview.html

Tool	Details
annotatebamwithumis	Annotates existing BAM files with UMIs (Unique Molecular Indices) from a separate FASTQ file
applybqsr	Apply BQSR report to a bam file and generate new bam file
arriba	Tool for the detection of gene fusions from RNA-Seq data
bam2fq	Convert a BAM to FASTQ
bammetrics	Collect WGS Metrics on a bam file
bamsort	Sort BAM file
bcftoolscall	Call variants from mpileup output
bcftoolsmpileup	Generate BCF/VCF pileup for one or multiple BAM files
bqsr	Collect BQSR report on a BAM file
cnnscorevariants	Generate variant scores using a Convolutional Neural Network
cnvkit	Run CNVkit with accelerated coverage calculation from read depths
collectmultiplemetrics	Collect multiple classes of metrics on a bam file
consensusreads	Calls consensus sequences from reads with the same unique molecular tag
dbsnp	Annotate variants based on a dbsnp
deeptrio	Run GPU-DeepTrio for calling de novo variants
deepvariant	Run GPU-DeepVariant for calling germline variants
demuxfastqs	Perform sample demultiplexing on FASTQs
expansionhunter	A tool for estimating large repeats in the bam
fq2bam	Run bwa mem, co-ordinate sorting, marking duplicates and Base Quality Score Recalibration
frequencyfiltration	Filter a VCF by allele frequency or allele count
genotypegvcf	Convert a GVCF to VCF
glnexus	Merge and joint-call input gVCF files, emitting multi-sample BCF
groupreadsbyumi	Groups reads together that appear to have come from the same original molecule
haplotypecaller	Run GPU-HaplotypeCaller for calling germline variants
indexgvcf	Index a GVCF file
kallisto	Quantify abundances of transcripts from bulk and single-cell RNA-Seq data
lofreq	Call variants with high sensitivity, predicting variants below the average base-call quality
manta	Analyze germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs
muse	Call somatic variants with accelerated MuSE variant caller
mutectcaller	Run GPU-Mutect2 for tumor-normal analysis
postpon	Generate the final vcf output of doing mutect pon
prepon	Build an index for pon file, which is the prerequisite to do mutect pon
rna_fq2bam	Run RNA-seq data through the fq2bam pipeline
samtoolsmpileup	Generate text pileup for one or multiple BAM files
setmateinfo	Adds and/or fixes mate information on paired-end reads
smoove	Call and genotype SVs for short reads
snpswift	Annotate variants in a VCF file with VCF or GTF databases.
somaticsniper	Identify single nucleotide positions that are different between tumor and normal BAM files
somaticsniper_workflow	Run the somaticsniper variant caller workflow
splitncigar	Split reads in a BAM file that contain Ns in their cigar string
starfusion	Identify candidate fusion transcripts supported by Illumina reads
strelka	Analyze germline variation in small cohorts and somatic variation in tumor/normal sample pairs
strelka_workflow	Run the strelka variant caller workflow
triocombinegvcf	Combine GVCF of 2 or 3 samples
umi_fgbio	This UMI pipeline is based on Fulcrum Genomics toolkit, processes sequencing reads with molecular barcodes (also known as Unique Molecular Indices, UMIs), which provide impressive error correction and increased accuracy using a sequencing consensus read level
variantfiltration	Filter a VCF using a boolean expression
vcfanno	Annotate a VCF using dbsnp and annotation files
vcfqc	Generate QC plots on a VCF file
vcfqcbybam	Generate a summaryfile using samtoolsmpileup that can be used for plotting/report generation
votebasedvcfmerger	Create union and intersection VCFs based on a minimum number of variant callers supporting a variant
vqsr	Build a recalibration model to score variant quality and apply a score cutoff to filter variants