Tools/Software Resources
Below is a table listing various software and other tools that are commonly used in genomics analyses. Most are mentioned throughout the PGC Video Textbook. Please use the outline below to navigate through the table.
- General Tools
- GWAS
- QC
- Imputation and haplotype phasing
- Relatedness/Population stratification
- Association testing
- Power testing
- PRS methods
- Post-GWAS analysis
- SNP heritability
- Genetic correlation
- TWAS
- PheWAS
- Gene/Gene set identification
- eQTLs
- Gene set enrichment
- Functionally-informed risk scores
- Fine-mapping
- Conditional analyses
- EWAS
- Mendelian Randomization
- WGS and WES analysis
- Raw count QC
- Preprocessing
- Alignment
- Post-alignment processing
- Variant calling (SNPs/INDELs)
- Variant calling (CNVs)
- Variant annotation
- Association testing
- Datasets and data access
- Other Genomics tools
- Genome Builds
| Analysis | Step | Software | Additional Tutorials | Language | PubMed ID |
|---|---|---|---|---|---|
General Tools |
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| General | File management/formatting | SAMtools | Manual | C; Python | 19505943; 21903627; 21320865 |
| General | File management/formatting | BCFtools | Manual; GitHub | C; Python | 19505943; 21903627; 21320865 |
| General | File management/formatting | BEDtools | GitHub | C; C++ | 20110278 |
GWAS |
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| GWAS | Genotype calling and Imputation | MoChA | GitHub | C; R | 29995854; 32581363 |
| GWAS | Rapid Imputation and Computational Pipeline for GWAS (RICOPILI) | RICOPILI pipeline | RICOPILI download; Tutorial | Perl; R | 31393554 |
| GWAS | General; QC | PLINK1.9/PLINK2 | PLINK website | C; C++ | 17701901 |
| GWAS | Relatedness/Kinship | KING | Manual; GENESIS documentation | 20926424 | |
| GWAS | Population Stratification/PCA | GENESIS/PCAiR | Manual; Tutorial; GENESIS GitHub | R | 20926424; 25810074; 31329242 |
| GWAS | Population Stratification/PCA | GENESIS/PC-Relate | Tutorial | R | 26748516 |
| GWAS | Local Ancestry and Admixture Inference | RFMix | GitHub | C++ | 23910464 |
| GWAS | Local Ancestry and Admixture Inference | TRACTOR | GitHub | Python | 33462486 |
| GWAS | Imputation panel | TOPMed | Imputation server | NA | 33568819 |
| GWAS | Imputation panel | 1000 Genomes | Imputation server | NA | 26432245 |
| GWAS | Imputation panel | HRC | Website | NA | 27548312 |
| GWAS | Imputation algorithm | minimac | GitHub | C++; C | 27571263 |
| GWAS | Haplotype phasing | EAGLE | Manual; GitHub | C++ | 27694958; 27270109 |
| GWAS | Phasing and Imputation | BEAGLE | Website; Tutorial | Java | 23535385; 30100085; 34478634 |
| GWAS | Haplotype phasing | SHAPEIT | Website; Tutorial; GitHub | C++ | 22138821; 23269371; 24094745; 24743097; 25653097 |
| GWAS | Power calculations | genpwr | Manual | R | 32721961 |
| GWAS | Association Testing | SAIGE | GitHub; More documentation | R; C++ | 30104761 |
| GWAS | Association Testing | BOLT-LMM | Download; Manual | 25642633 | |
| GWAS | Association Testing | REGENIE | GitHub; Tutorial | C++ | 34017140 |
| GWAS | Causal Mixture Model | MiXeR | GitHub | C | 32427991; 31160569 |
| GWAS | Multi-Trait Analysis of GWAS | MTAG | GitHub | Python | 29292387 |
| GWAS | qqplot and Manhattan plot | qqman | GitHub | R | doi link |
| GWAS | QC of GWAS summary statistics | DENTIST | GitHub; Yang Lab Website | C++ | 34880243 |
| GWAS | GWAS Quality Score | GQS | GitHub | Python | 36651666 |
PRS Methods |
|||||
| PRS | PRS methods | PRS-CS | GitHub | Python | 30992449 |
| PRS | PRS methods | PRS-CSx | GitHub | Python | 35513724 |
| PRS | PRS methods | PRSice2 | Tutorial | R | 31307061 |
| PRS | PRS methods | Lassosum | GitHub | R; C++ | 28480976 |
| PRS | PRS methods | LDpred2 | Manual | R | 33326037 |
| PRS | PRS methods | SBayesR | Manual | 31704910 | |
| PRS | PRS methods | MegaPRS | Python | 34234142 | |
Post-GWAS Analyses |
|||||
| SNP heritability | GCTA-GREML | Tutorial; GitHub | C++ | 27457963 | |
| SNP heritability and genetic correlation | Linkage Disequilibrium Score Regression | LDSC | Tutorial; GitHub | Python | 25642630 |
| Genetic correlation | Genomic Structural Equation Modeling | Genomic SEM | Tutorial; GitHub | R | 30962613 |
| Genetic correlation | LAVA | GitHub | R | 35288712 | |
| TWAS | Functional Summary-based Imputation | FUSION | GitHub; Tutorial | R | 26854917 |
| TWAS | Transcriptomic Imputation | PrediXcan | GitHub; Tutorial | Python | 26258848 |
| TWAS | Transcriptomic Imputation | S-PrediXcan | GitHub | Python | 29739930 |
| TWAS | Tissue models (GTEx, CommonMind, PsychENCODE) | PredictDB | GTEx models; PsychENCODE models; CommonMind DLPFC models | NA | 33499903; 30545856; 30911161 |
| TWAS/MR | Summary-data-based Mendelian Randomization | SMR | Software | 27019110 | |
| PheWAS | Phenome-Wide Association Studies | PheWAS R package | GitHub; Tutorial | R | 20335276; 24733291; 24270849 |
| Gene/Gene set identification | Gene Set Enrichment Analysis | GSEA | Documentation; README | Java; R | 16199517; 12808457 |
| Gene/Gene set identification | Molecular Signatures Database | MsigDB | Documentation | Java | 16199517; 21546393; 26771021 |
| Gene/Gene set identification | Generalized gene-set analysis of GWAS data | MAGMA | Software; Tutorial; Manual | 25885710; 27070863; 30218068 | |
| Gene/Gene set identification | HiC-informed gene-based tests | H-MAGMA | GitHub | R | 32152537 |
| Gene/Gene set identification | eQTL-informed gene-based tests | E-MAGMA | GitHub Tutorial | 33624746 | |
| Gene/Gene set identification | Functional Mapping and Annotation of Genome-Wide Association Studies | FUMA | GitHub; Tutorial | Blade; Java | 29184056 |
| Gene/Gene set identification | Set/Pathway-based analysis | PRSet | Tutorial | R | 36749789 |
| Gene/Gene set identification | Gene set enrichment | g:profiler | Website; R package; Documentation | R | 31066453 |
| eQTLs | eQTL and GWAS CAusal Variants Identification in Associated Regions | eCAVIAR | Website; GitHub | C++ | 27866706 |
| eQTLs | Calling eQTLs | fastQTL | GitHub; Documentation | C++ | 26708335 |
| eQTLs | Calling eQTLs | matrixQTL | Tutorial; GitHub | R | 22492648 |
| Functionally-informed Risk Scores | Polygenic Transcriptomic Risk Score | PTRS | GitHub; Calculate PTRS for UKBB | Python | 35027082 |
| Functionally-informed Risk Scores | Trans-ethnic polygenic risk scores | PolyPred/PolyPred+ | GitHub; Tutorial; Documentation | Python | 35393596 |
| Fine-mapping | “Sum of Single Effects” model | SuSiE (used with coloc) | R package | R | 37220626; 34587156 |
| Fine-mapping | Co-localization analysis | coloc | GitHub; R package | R | 24830394; 32310995; 34587156 |
| Fine-mapping | CAusal Variants Identification in Associated Regions | CAVIAR | Website; GitHub | C++ | 25104515 |
| Fine-mapping | FINEMAP | Benner lab website; FinnGen pipeline | Python; WDL | 26773131 | |
| Fine-mapping | Integrative Genetic Association Analysis using Deterministic Approximation of Posteriors | DAP-G | GitHub; Manual | C++ | 27236919 |
| Conditional analyses | Multi-SNP-based conditional and joint association analysis using GWAS summary data | GCTA-COJO | Website; GCTA GitHub | C++ | 22426310 |
| Conditional analyses | Multi-trait-based conditional and joint analysis using GWAS summary data | GCTA-mtCOJO | Website; GCTA GitHub | C++ | 32398722 |
| EWAS | Epigenome-Wide Association Study | ewastools | GitHub; Workflow | R | |
| Mendelian Randomization | 2-sample MR using MR-Base database | TwoSampleMR | GitHub; Website | R | 29846171; 29149188 |
| Mendelian Randomization | Database and analytical platform for MR | MR-Base | WebApp; R package (TwoSampleMR); OpenGWAS database | R | 29846171 |
Sequencing Tools |
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| WGS/WES | Raw count QC | FastQC | GitHub | Java | |
| WGS/WES | Raw count QC | MultiQC | GitHub | Python | 27312411 |
| WGS/WES | Raw count QC | NGS QC Toolkit | GitHub | Perl | 22312429 |
| WGS/WES | Raw count QC | QC-Chain | GitHub | WDL | 23565205 |
| WGS/WES | Preprocessing | TrimGalore | GitHub; Documentation | Perl | |
| WGS/WES | Preprocessing | Cutadapt | GitHub; Documentation | Python | |
| WGS/WES | Preprocessing | Btrim | Website | C | 21651976 |
| WGS/WES | Preprocessing | Trimmonatic | GitHub | Java | 24695404 |
| WGS/WES | Preprocessing | leeHom | GitHub; Documentation | C++ | 25100869 |
| WGS/WES | Alignment | BWA/BWA-mem | GitHub | C | 19451168; 20080505 |
| WGS/WES | Alignment | Minimap2 | GitHub | C; Java; TeX | 29750242 |
| WGS/WES | Alignment | Bowtie2 | GitHub | C++; Perl | 22388286 |
| WGS/WES | Alignment | GATK | Website; GitHub | Java | Book citation: Van der Auwera GA & O’Connor BD. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (1st Edition). O’Reilly Media. |
| WGS/WES | Alignment | Cactus | GitHub | C; Python | 33177663 |
| WGS/WES | Alignment | Giraffe | GitHub | C++ | |
| WGS/WES | Post-alignment processing | Picard (MarkDuplicates) | GitHub; Website; Tutorial | Java | |
| WGS/WES | Post-alignment processing | GATK (see above links in “Alignment”) | |||
| WGS/WES | Variant calling (SNPs/INDELs) | WeCall | GitHub | C++; Python | |
| WGS/WES | Variant calling (SNPs/INDELs) | GATK HaplotypeCaller | Website | Java | |
| WGS/WES | Variant calling (SNPs/INDELs) | Picard | Website; GitHub | Java | |
| WGS/WES | Variant calling (SNPs/INDELs) | FreeBayes | GitHub | C++ | |
| WGS/WES | Variant calling (SNPs/INDELs) | DeepVariant | GitHub | Python; C++ | |
| WGS/WES | Variant calling (SNPs/INDELs) | Slivar | GitHub | Nim; HTML; Java | |
| WGS/WES | Variant calling (CNVs) | Parliament2 | GitHub; Documentation | Python; C++; C | 33347570 |
| WGS/WES | Variant calling (CNVs) | muCNV | GitHub | C++; C | 33760063 |
| WGS/WES | Variant calling (CNVs) | TT-Mars | GitHub | Python | 35524317 |
| WGS/WES | Variant calling (CNVs) | Truvari | GitHub | Python | 36575487 |
| WGS/WES | Variant calling (CNVs) | XHMM | Manual; Tutorial | C++ | 24763994 |
| WGS/WES | Variant calling (CNVs) | CODEX | GitHub | R | 25618849 |
| WGS/WES | Variant calling (CNVs) | DECA | GitHub | Scala; R | 31604420 |
| WGS/WES | Variant calling (CNVs) | CLAMMS | GitHub | C | 26382196 |
| WGS/WES | Variant calling (CNVs) | cn.MOPS | GitHub | R | 22302147 |
| WGS/WES | Variant calling (CNVs) | GATK-gCNV | GitHub; Tutorial | Python; WDL | Babadi, et. al (2022), BioRxiv |
| WGS/WES | Variant calling (CNVs) | ReadDepth | GitHub | R | 21305028 |
| WGS/WES | Variant calling (CNVs) | ERDS | GitHub | Perl; C | 22939633 |
| WGS/WES | Variant annotation | gnomAD | Website | NA | 32461654 |
| WGS/WES | Variant annotation | SnpEff | GitHub | Java | 22728672 |
| WGS/WES | Variant annotation | Hail | Website | ||
| WGS/WES | Variant annotation | SnpSift | GitHub | Java | 22435069 |
| WGS/WES | Variant annotation | ClinVar | Website | NA | |
| WGS/WES | Variant annotation | Human Gene Mutation Database (HGMD) | HGMD Website | NA | |
| WGS/WES | Variant annotation | dbSNP | Website | NA | |
| WGS/WES | Variant annotation | dbNSFP | Website | NA | 21520341 |
| WGS/WES | Variant annotation | SIFT | Website | NA | 22689647 |
| WGS/WES | Variant annotation | Polyphen2 | Website | NA | 20354512 |
| WGS/WES | Variant annotation | MutationTaster | Website | NA | 24681721 |
| WGS/WES | Variant annotation | Combined Annotation Dependent Depletion (CADD) | CADD website | NA | 30371827 |
| WGS/WES | Variant annotation | CONsensus DELeteriousness (CONDEL) | CONDEL website | NA | |
| WGS/WES | Variant annotation | Multivariate Analysis of Protein Polymorphism(MAPP) | MAPP website | NA | 15965030 |
| WGS/WES | Variant annotation | MutationAssessor | Website | NA | 21727090 |
| WGS/WES | Variant annotation | ANNOVAR | Website | Perl | 20601685 |
| WGS/WES | Variant annotation | Variant Effect Predictor (VEP) | VEP Website | Perl | 27268795 |
| WGS/WES | Variant annotation | SeattleSeq | Website | NA | 19684571 |
| WGS/WES | Variant annotation | ClinGen | Website | ||
| WGS/WES | Variant annotation | X-CNV | GitHub; Documentation | R | 34407882 |
| WGS/WES | Variant annotation | AnnotSV | GitHub; Documentation | TCL; Python | 29669011 |
| WGS/WES | Association Testing | EPACTS | GitHub; Documentation | C++ | |
| WGS/WES | Association Testing | BOLT-LMM | Download; Manual | 25642633 | |
| WGS/WES | Association Testing | REGENIE | GitHub; Tutorial | C++ | 34017140 |
| WGS/WES | Association Testing | SNP-Set (Sequence) Kernal Association Test (SKAT) | SKAT Documentation; Website | R | 23684009 |
| WGS/WES | Association Testing | SAIGE | GitHub; More documentation | R; C++ | 30104761 |
| WGS/WES | Association Testing | Generalized linear Mixed Model Association Tests (GMMAT) | GitHub | C; R; C++ | 27018471 |
| WGS/WES | Association Testing | CoCoRV (Rare variant tests) | GitHub | C++ | 35545612 |
| WGS/WES | Additional tools | GLnexus | GitHub | C++ | |
Datasets/Data Access |
|||||
| 1000 Genomes | |||||
| dbGAP (US) | |||||
| FinnGen | |||||
| GTEx | |||||
| GWAS Catalog | |||||
| NIMH repository (US) | |||||
| PGC Summary Statistics | |||||
| PsychENCODE | |||||
| PsychSCREEN | |||||
Other Genomics Tools |
|||||
| Ensembl | Genome browser for annotation, alignment, and other tools | ||||
| BioMart R package | R tool for pulling annotation information from Ensembl and other large databases | Documentation | R | ||
| LiftOver | Tool for converting genome coordinates | ||||
| UCSC Browser | Tools for visualizing genomic data, aligning sequences | ||||
| Genecards | Database for information on annotated and predicted human genes | ||||
Genome Builds |
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| GRCh38.p14 | Latest genome build from Genome Reference Consortium (GRC) Build release (2022) |
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| GRCh38/hg38 | Build release (2013) | ||||
| GRCh37/hg19 | Build release (2009) |