| applybqsr | Apply BQSR report to a BAM file and generate a new BAM file |
| bam2fq | Convert a BAM file to FASTQ |
| bammetrics | Collect WGS Metrics on a BAM file |
| bamsort | Sort a BAM file |
| bqsr | Collect BQSR report on a BAM file |
| collectmultiplemetrics | Collect multiple classes of metrics on a BAM file |
| dbsnp | Annotate variants based on a dbsnp |
| deepsomatic | Run GPU-DeepSomatic for calling somatic variants |
| deepvariant | Run GPU-DeepVariant for calling germline variants |
| deepvariant_germline | Run the germline pipeline from FASTQ to VCF using a deep neural network analysis |
| fq2bam (BWA-MEM + GATK) | Run bwa mem, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration |
| fq2bam_meth | Run GPU-accelerated bwa-meth compatible alignment, co-ordinate sorting, marking duplicates, and Base Quality Score Recalibration |
| genotypegvcf | Convert a GVCF to VCF |
| germline (GATK Germline Pipeline) | Run the germline pipeline from FASTQ to VCF |
| giraffe (vg giraffe + GATK) | Run GPU-accelerated VG-giraffe compatible pangenome alignment and co-ordinate sorting |
| haplotypecaller | Run GPU-HaplotypeCaller for calling germline variants |
| indexgvcf | Index a GVCF file |
| markdup | Identifies duplicate reads |
| minimap2 | Align long read sequences against a large reference database to convert FASTQ to BAM/CRAM |
| mutectcaller | Run GPU-Mutect2 for tumor-normal analysis |
| ont_germline | Run the germline pipeline from FASTQ/BAM to VCF by aligning long read ONT sequences with minimap2 and using a deep neural network analysis |
| pacbio_germline | Run the germline pipeline from FASTQ/BAM to VCF by aligning long read sequences with minimap2 and using a deep neural network analysis |
| pangenome_aware_deepvariant | Run GPU-Pangenome-aware-deepvariant that uses a pangenome reference for calling germline variants |
| pangenome_germline | Run the germline pipeline from FASTQ to VCF using pangenome alignment (Giraffe) and pangenome-aware DeepVariant |
| postpon | Generate the final VCF output of doing mutect pon |
| prepon | Build an index for PON file, which is the prerequisite to performing mutect pon |
| rna_fq2bam | Run RNA-seq data through the fq2bam pipeline |
| somatic (Somatic Variant Caller) | Run the somatic pipeline from FASTQ to VCF |
| starfusion | Identify candidate fusion transcripts supported by Illumina reads |
