Mosdepth: quick coverage calculation for genomes and exomes von Pedersen, Brent S, Quinlan, Aaron R

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A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar von Garrison, Erik, Kronenberg, Zev N, Dawson, Eric T, Pedersen, Brent S, Prins, Pjotr

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A map of constrained coding regions in the human genome von Havrilla, James M., Pedersen, Brent S., Layer, Ryan M., Quinlan, Aaron R.

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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations von Dale, Ryan K., Pedersen, Brent S., Quinlan, Aaron R.

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GIGGLE: a search engine for large-scale integrated genome analysis von Layer, Ryan M, Pedersen, Brent S, DiSera, Tonya, Marth, Gabor T, Gertz, Jason, Quinlan, Aaron R

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Samplot: a platform for structural variant visual validation and automated filtering von Belyeu, Jonathan R, Chowdhury, Murad, Brown, Joseph, Pedersen, Brent S, Cormier, Michael J, Quinlan, Aaron R, Layer, Ryan M

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The nasal methylome and childhood atopic asthma von Yang, Ivana V., PhD, Pedersen, Brent S., PhD, Liu, Andrew H., MD, O'Connor, George T., MD, Pillai, Dinesh, MD, Kattan, Meyer, MD, Misiak, Rana Tawil, MD, Gruchalla, Rebecca, MD, Szefler, Stanley J., MD, Khurana Hershey, Gurjit K., MD, PhD, Kercsmar, Carolyn, MD, Richards, Adam, PhD, Stevens, Allen D., BA, Kolakowski, Christena A., MS, Makhija, Melanie, MD, Sorkness, Christine A., PharmD, Krouse, Rebecca Z., MS, Visness, Cynthia, PhD, Davidson, Elizabeth J., BA, Hennessy, Corinne E., BS, Martin, Richard J., MD, Togias, Alkis, MD, Busse, William W., MD, Schwartz, David A., MD

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DNA methylation and childhood asthma in the inner city von Yang, Ivana V., PhD, Pedersen, Brent S., PhD, Liu, Andrew, MD, O'Connor, George T., MD, Teach, Stephen J., MD, MPH, Kattan, Meyer, MD, Misiak, Rana Tawil, MD, Gruchalla, Rebecca, MD, Steinbach, Suzanne F., MD, Szefler, Stanley J., MD, Gill, Michelle A., MD, PhD, Calatroni, Agustin, MA, MS, David, Gloria, PhD, MHSc, Hennessy, Corinne E., BS, Davidson, Elizabeth J., BA, Zhang, Weiming, PhD, Gergen, Peter, MD, MPH, Togias, Alkis, MD, Busse, William W., MD, Schwartz, David A., MD

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Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation von Sasani, Thomas A, Pedersen, Brent S, Gao, Ziyue, Baird, Lisa, Przeworski, Molly, Jorde, Lynn B, Quinlan, Aaron R

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Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls von Pedersen, Brent S, Quinlan, Aaron R

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Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs von Woodhouse, Margaret R, Schnable, James C, Pedersen, Brent S, Lyons, Eric, Lisch, Damon, Subramaniam, Shabarinath, Freeling, Michael

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Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies von Cormier, Michael J, Pedersen, Brent S, Bayrak-Toydemir, Pinar, Quinlan, Aaron R

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STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci von Dashnow, Harriet, Pedersen, Brent S, Hiatt, Laurel, Brown, Joe, Beecroft, Sarah J, Ravenscroft, Gianina, LaCroix, Amy J, Lamont, Phillipa, Roxburgh, Richard H, Rodrigues, Miriam J, Davis, Mark, Mefford, Heather C, Laing, Nigel G, Quinlan, Aaron R

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Relationship of DNA methylation and gene expression in idiopathic pulmonary fibrosis von Yang, Ivana V, Pedersen, Brent S, Rabinovich, Einat, Hennessy, Corinne E, Davidson, Elizabeth J, Murphy, Elissa, Guardela, Brenda Juan, Tedrow, John R, Zhang, Yingze, Singh, Mandal K, Correll, Mick, Schwarz, Marvin I, Geraci, Mark, Sciurba, Frank C, Quackenbush, John, Spira, Avrum, Kaminski, Naftali, Schwartz, David A

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Combating subclonal evolution of resistant cancer phenotypes von Brady, Samuel W., McQuerry, Jasmine A., Qiao, Yi, Piccolo, Stephen R., Shrestha, Gajendra, Jenkins, David F., Layer, Ryan M., Pedersen, Brent S., Miller, Ryan H., Esch, Amanda, Selitsky, Sara R., Parker, Joel S., Anderson, Layla A., Dalley, Brian K., Factor, Rachel E., Reddy, Chakravarthy B., Boltax, Jonathan P., Li, Dean Y., Moos, Philip J., Gray, Joe W., Heiser, Laura M., Buys, Saundra S., Cohen, Adam L., Johnson, W. Evan, Quinlan, Aaron R., Marth, Gabor, Werner, Theresa L., Bild, Andrea H.

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Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy von Tang, Haibao, Woodhouse, Margaret R, Cheng, Feng, Schnable, James C, Pedersen, Brent S, Conant, Gavin, Wang, Xiaowu, Freeling, Michael, Pires, J Chris

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CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing von Wallace, Amelia D, Sasani, Thomas A, Swanier, Jordan, Gates, Brooke L, Greenland, Jeff, Pedersen, Brent S, Varley, Katherine E, Quinlan, Aaron R

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Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches von Pedersen, Brent S, Bhetariya, Preetida J, Brown, Joe, Kravitz, Stephanie N, Marth, Gabor, Jensen, Randy L, Bronner, Mary P, Underhill, Hunter R, Quinlan, Aaron R

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Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data von Cormier, Michael J., Belyeu, Jonathan R., Pedersen, Brent S., Brown, Joseph, Köster, Johannes, Quinlan, Aaron R.

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Effective variant filtering and expected candidate variant yield in studies of rare human disease von Pedersen, Brent S., Brown, Joe M., Dashnow, Harriet, Wallace, Amelia D., Velinder, Matt, Tristani-Firouzi, Martin, Schiffman, Joshua D., Tvrdik, Tatiana, Mao, Rong, Best, D. Hunter, Bayrak-Toydemir, Pinar, Quinlan, Aaron R.

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