From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895

ggplot2: Elegant Graphics for Data Analysis

Wickham, H. (2009) · doi:10.1007/978-0-387-98141-3 · Cited by 14,447

On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other

Mann, H. B., & Whitney, D. R. (1947) · The Annals of Mathematical Statistics · doi:10.1214/aoms/1177730491 · Cited by 14,320

Fast and accurate long-read alignment with Burrows-Wheeler transform.

Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063

A framework for variation discovery and genotyping using next-generation DNA sequencing data

DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457

A map of human genome variation from population-scale sequencing.

The 1000 Genomes Project Consortium (2010) · Nature · doi:10.1038/nature09534 · Cited by 7,877

dbSNP: the NCBI database of genetic variation

Sherry, S. T. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.308 · Cited by 7,502

Integrating common and rare genetic variation in diverse human populations

The International HapMap 3 Consortium (2010) · Nature · doi:10.1038/nature09298 · Cited by 3,026

Functional characterization of tektin-1 in motile cilia and evidence for TEKT1 as a new candidate gene for motile ciliopathies

Ryan, R., Failler, M., Reilly, M. L., Garfa-Traore, M., Delous, M., Filhol, E., Reboul, T., Bole-Feysot, C., Nitschké, P., Baudouin, V., et al. (2018) · Human Molecular Genetics · doi:10.1093/hmg/ddx396 · Cited by 48

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

Natri, H. M., Bobowik, K. S., Kusuma, P., Crenna Darusallam, C., Jacobs, G. S., Hudjashov, G., Lansing, J. S., Sudoyo, H., Banovich, N. E., Cox, M. P., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008749 · Cited by 48

Parasex Generates Phenotypic Diversity de Novo and Impacts Drug Resistance and Virulence in Candida albicans

Hirakawa, M. P., Chyou, D. E., Huang, D., Slan, A. R., & Bennett, R. J. (2017) · Genetics · doi:10.1534/genetics.117.300295 · Cited by 47

Genes and pathways implicated in tetralogy of Fallot revealed by ultra-rare variant burden analysis in 231 genome sequences

Manshaei, R., Merico, D., Reuter, M. S., Engchuan, W., Mojarad, B. A., Chaturvedi, R., Heung, T., Pellecchia, G., Zarrei, M., Nalpathamkalam, T., et al. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.00957 · Cited by 36

Genome sequencing in persistently unsolved white matter disorders

Helman, G., Lajoie, B. R., Crawford, J., Takanohashi, A., Walkiewicz, M., Dolzhenko, E., Gross, A. M., Gainullin, V. G., Bent, S. J., Jenkinson, E. M., et al. (2020) · Annals of Clinical and Translational Neurology · doi:10.1002/acn3.50957 · Cited by 39

The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels

Axelsson, E., Ljungvall, I., Bhoumik, P., Conn, L. B., Muren, E., Ohlsson, Å., Olsen, L. H., Engdahl, K., Hagman, R., Hanson, J., et al. (2021) · PLOS Genetics · doi:10.1371/journal.pgen.1009726 · Cited by 34

Acquisition of cross-azole tolerance and aneuploidy in Candida albicans strains evolved to posaconazole

Kukurudz, R. J., Chapel, M., Wonitowy, Q., Adamu Bukari, A.-R., Sidney, B., Sierhuis, R., & Gerstein, A. C. (2022) · G3 · doi:10.1093/g3journal/jkac156 · Cited by 35

Genomic instability in the naturally and prematurely aged myocardium

De Majo, F., Martens, L., Hegenbarth, J.-C., Rühle, F., Hamczyk, M. R., Nevado, R. M., Andrés, V., Hilbold, E., Bär, C., Thum, T., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2022974118 · Cited by 35

Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries

Natri, H. M., Hudjashov, G., Jacobs, G., Kusuma, P., Saag, L., Darusallam, C. C., Metspalu, M., Sudoyo, H., Cox, M. P., Gallego Romero, I., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.11.017 · Cited by 33

Whole-Exome Sequencing for Diagnosis of Turner Syndrome: Toward Next-Generation Sequencing and Newborn Screening

Murdock, D. R., Donovan, F. X., Chandrasekharappa, S. C., Banks, N., Bondy, C., Muenke, M., & Kruszka, P. (2017) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/jc.2016-3414 · Cited by 34

Advancing diagnosis and management of liver disease in adults through exome sequencing

Zheng, M., Hakim, A., Konkwo, C., Deaton, A. M., Ward, L. D., Silveira, M. G., Assis, D. N., Liapakis, A., Jaffe, A., Jiang, Z. G., et al. (2023) · EBioMedicine · doi:10.1016/j.ebiom.2023.104747 · Cited by 34

Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma

Mitra, A., Andrews, M. C., Roh, W., De Macedo, M. P., Hudgens, C. W., Carapeto, F., Singh, S., Reuben, A., Wang, F., Mao, X., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15538-9 · Cited by 27

Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals

Yang, J.-H., Griffin, P. T., Vera, D. L., Apostolides, J. K., Hayano, M., Meer, M. V., Salfati, E. L., Su, Q., Munding, E. M., Blanchette, M., et al. (2019) · doi:10.1101/808642 · Cited by 38

Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution

Monberg, M. E., Geiger, H., Lee, J. J., Sharma, R., Semaan, A., Bernard, V., Wong, J., Wang, F., Liang, S., Swartzlander, D. B., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31376-3 · Cited by 30

FixItFelix: improving genomic analysis by fixing reference errors

Behera, S., LeFaive, J., Orchard, P., Mahmoud, M., Paulin, L. F., Farek, J., Soto, D. C., Parker, S. C. J., Smith, A. V., Dennis, M. Y., et al. (2023) · Genome Biology · doi:10.1186/s13059-023-02863-7 · Cited by 28

Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases

Kobren, S. N., Baldridge, D., Velinder, M., Krier, J. B., LeBlanc, K., Esteves, C., Pusey, B. N., Züchner, S., Blue, E., Lee, H., et al. (2021) · Genetics in Medicine · doi:10.1038/s41436-020-01084-8 · Cited by 27

Standing variation rather than recent adaptive introgression probably underlies differentiation of the texanus subspecies of Helianthus annuus

Owens, G. L., Todesco, M., Bercovich, N., Légaré, J., Mitchell, N., Whitney, K. D., & Rieseberg, L. H. (2021) · Molecular Ecology · doi:10.1111/mec.16008 · Cited by 20

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection

Le Luyer, J., Schull, Q., Auffret, P., Lopez, P., Crusot, M., Belliard, C., Basset, C., Carradec, Q., Poulain, J., Planes, S., et al. (2021) · Animal Microbiome · doi:10.1186/s42523-021-00097-1 · Cited by 16

High performance of a GPU-accelerated variant calling tool in genome data analysis

Zhang, Q., Liu, H., & Bu, F. (2021) · doi:10.1101/2021.12.12.472266 · Cited by 13

Can a Liquid Biopsy Detect Circulating Tumor DNA With Low-passage Whole-genome Sequencing in Patients With a Sarcoma? A Pilot Evaluation

Anderson, C. J., Yang, H., Parsons, J., Ahrens, W. A., Jagosky, M. H., Hsu, J. H., Patt, J. C., Kneisl, J. S., & Steuerwald, N. M. (2025) · Clinical Orthopaedics & Related Research · doi:10.1097/corr.0000000000003161 · Cited by 10

Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression

Nassiri, I., Kwok, A. J., Bhandari, A., Bull, K. R., Garner, L. C., Klenerman, P., Webber, C., Parkkinen, L., Lee, A. W., Wu, Y., et al. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae085 · Cited by 8

Evaluation of chromatin accessibility in prefrontal cortex of schizophrenia cases and controls

Bryois, J., Garrett, M. E., Song, L., Safi, A., Giusti-Rodriguez, P., Johnson, G. D., Demur, A. B., Fullard, J. F., Roussos, P., Sklar, P., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/141986 · Cited by 7

Chromosomal-level reference genome assembly of the North American wolverine (Gulo gulo luscus): a resource for conservation genomics

Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Wintle, R. F., Engstrom, M. D., Stacy, E., Waits, L. P., Scrafford, M., & Scherer, S. W. (2022) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkac138 · Cited by 6

Chromosomal-level reference genome assembly of muskox (Ovibos moschatus) from Banks Island in the Canadian Arctic, a resource for conservation genomics

Lok, S., Lau, T. N. H., Trost, B., Tong, A. H. Y., Paton, T., Wintle, R. F., Engstrom, M. D., Gunn, A., & Scherer, S. W. (2024) · Scientific Reports · doi:10.1038/s41598-024-67270-9 · Cited by 4

Novel LRP6 Mutations Causing Non-Syndromic Oligodontia

Lee, Y., Chae, W., Kim, Y. J., & Kim, J.-W. (2022) · Journal of Personalized Medicine · doi:10.3390/jpm12091401 · Cited by 4

FLNC -Related Cardiomyopathies in an Admixed Population: Expanding the Genotype-Phenotype Spectrum and Clinical Correlates

Olivetti, N. Q. S., Sacilotto, L., Ferreira, J. D. B. N., Furquim, S., Pagotti, M., Santos, B. M., Mizuta, M., Senra, P. D. M., Napolitano, G., Vilalva, K., et al. (2026) · Circulation: Genomic and Precision Medicine · doi:10.1161/circgen.126.005733

Whole‐Genome Sequencing and Single‐Cell Transcriptomics Identify Human Leukocyte Antigen Loci and a COG5 Variant in Aortic Dissection

Lin, J., Wu, S., Lin, C., Jin, S., Chen, L., Luo, J., Xu, S., Jin, L., Yu, M., Zheng, Y., et al. (2026) · Journal of the American Heart Association · doi:10.1161/jaha.126.050327

GATK Variant Discovery Pipeline

He, C., & Liu, S. (2024) · BIO-PROTOCOL · doi:10.21769/bioprotoc.5068

Validation and assessment of variant calling pipelines for next-generation sequencing

Pirooznia, M., Kramer, M., Parla, J. S., Goes, F. S., Potash, J. B., McCombie, W. R., & Zandi, P. P. (2014) · Human Genomics · doi:10.1186/1479-7364-8-14 · Cited by 132

Variant Calling from RNA-seq Data Using the GATK Joint Genotyping Workflow

Brouard, J., & Bissonnette, N. (2012) · Methods in molecular biology · doi:10.1007/978-1-0716-2293-3_13 · Cited by 34

xGAP: a python based efficient, modular, extensible and fault tolerant genomic analysis pipeline for variant discovery

Gorla, A., Jew, B., Zhang, L., & Sul, J. H. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btaa1097 · Cited by 2

MapCaller – An integrated and efficient tool for short-read mapping and variant calling using high-throughput sequenced dataPreprint

Lin, H.-N., & Hsu, W. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/783605 · Cited by 6