| GEMMA | Application of linear mixed models and related models to GWAS | [4] |
| PLINK | Run association analyses and perform QC and regression steps | [5] |
| FastQC | Quality control checks on raw sequence data | [9] |
| Trimmomatic | Trim and crop FASTQ data | [10] |
| Cutadapt | finds and removes adapter sequences, primers, poly-A tails | [11] |
| BWA-MEM | produce multiple primary alignments for different part of a query sequence | [12] |
| Bowtie2 | aligning sequencing reads to long reference sequences | [13] |
| Samtools | Manipulate alignments in the SAM, BAM, and CRAM formats | [14] |
| GATK | Variant calling using sequencing data | [15] |
| VCFtools | Summarize, filter out, convert data into other file formats | [16] |
| FreeBayes | Bayesian genetic variant detector designed to fine SNPs | [17] |
| SnpEff | Annotation on genetic variants and predicts their effects on genes | [18] |
| ANNOVAR | Generate gene-based annotation | [19] |
| IGV | Visualization tool to simultaneously integrate and anlyze multiple types of genomic data | [20] |
| GenomeStudio | Normalize, cluster, and call genotypes | [25] |
| SVS | Perform analyses and visualizations on genomic and phenotypic data | [33] |
| BEAGLE | Genotype calling, phasing, and genotype imputation | [39] |
| Fimpute | Haplotype estimation or phasing and genotype imputation | [40] |
| Impute2 | Genotype imputation and haplotype phasing | [47] |
| Minimac | performs imputation with pre-phased haplotypes | [48] |