Table 1. Tools commonly used in genomic variant calling workflows.
| Workflow Task | Bioinformatics tools |
|---|---|
| Alignment | BWA MEM [32], Novoalign [33], Bowtie2 [34]† |
| Soringt SAM | Novosort [33], Samtools [35], Sambamba [36]† |
| Marking duplicates | Samblaster [37], Novosort [33], Picard [38] |
| Indel Realignment‡ | GATK [39] |
| Base Recalibration | |
| Variant Calling | GATK HaplotypeCaller [40] or UnifiedGenotyper, Samtools mpileup† [35], Platypus† [41], Strelka2† [42] |
| Joint Genotyping | GATK GenotypeGVCFs |
† Options absent from our implementation
‡ Indel realignment is not necessary past GATK version 3.6, but can be included to comply with legacy analyses, and to enable the use of non-GATK variant callers that require realignment.