Results 231 to 240 of about 37,179 (261)

A blended genome and exome sequencing method captures genetic variation in an unbiased and cost-effective manner. [PDF]

Nat Genet
Boltz TA, Chu BB, DeFelice M, Liao C, Sealock JM, Ye R, Goldstein JI, Majara L, Fu JM, Service SK, Zhan L, Medland SE, Chapman SB, Rubinacci S, Grimsby JL, Abebe T, Alemayehu M, Ashaba FK, Atkinson EG, Bigdeli TB, Bradway AB, Brand H, Chibnik LB, DeLuca S, Diaz-Zuluaga AM, Fekadu A, Gatzen M, Gelaye B, Gichuru S, Gildea ML, Hill TC, Huang H, Hubbard KM, Injera WE, James R, Joloba M, Kachulis C, Kalmbach PR, Kamulegeya R, Kigen G, Kim S, Koen N, Kwobah EK, Kyebuzibwa J, Lee S, Lennon NJ, Lind PA, Lopera-Maya EA, Makale J, Mangul S, McMahon J, Mowlem P, Musinguzi H, Mwema RM, Nakasujja N, Newman CP, Nkambule LL, O'Neil CR, Olivares AM, Olsen CM, Ongeri L, Parsa SJ, Pretorius A, Qin S, Ramesar R, Reagan FL, Sabatti C, Schneider JA, Shiferaw W, Stevens C, Stevenson A, Stricker E, Stroud RE, Tang J, Townsend M, Whiteman D, Yohannes MT, Yu M, Yuan K, NeuroGAP-Psychosis Study, Akena D, Atwoli L, Kariuki SM, Koenen KC, Newton CRJC, Stein DJ, Teferra S, Zingela Z, Pato CN, Pato MT, Lopez-Jaramillo C, Freimer NB, Ophoff RA, Olde Loohuis LM, Talkowski ME, Neale BM, Howrigan DP, Martin AR.   +97 more
europepmc   +1 more source

Molecular Evolution of a Sex-Linked Inversion Polymorphism in Zebra Finches. [PDF]

Genome Biol Evol
Price PD, Pepper J, Rogers TF, Wright AE, Slate J.   +4 more
europepmc   +1 more source

Variant calling comparison CASAVA1.8 and GATK

Nature Precedings, 2011
AbstractThis work aims at addressing the question of whether the new CASAVA1.8, which boasts improvements such as local realignments of reads, is at par with the well accepted pipeline of BWA mapping, duplicate removal, local realignment, re-calibration and variant calling using GATK.
Denis Bauer, Denis Bauer
exaly   +4 more sources

Efficient Acceleration of the Pair-HMMs Forward Algorithm for GATK HaplotypeCaller on Graphics Processing Units [PDF]

Evolutionary Bioinformatics, 2018
GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time.
Zaid Al-Ars, Koen Bertels
exaly   +8 more sources

Optimized pipeline of MuTect and GATK tools to improve the detection of somatic single nucleotide polymorphisms in whole-exome sequencing data [PDF]

BMC Bioinformatics, 2016
Detecting somatic mutations in whole exome sequencing data of cancer samples has become a popular approach for profiling cancer development, progression and chemotherapy resistance. Several studies have proposed software packages, filters and parametrizations. However, many research groups reported low concordance among different methods.
Giorgia Simonetti, Isabella Zironi, Cristina Papayannidis   +2 more
exaly   +10 more sources

RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK [PDF]

G3: Genes, Genomes, Genetics, 2015
Abstract Recent advances in variant calling made available in the Genome Analysis Toolkit (GATK) enable the use of validated single-nucleotide polymorphisms and indels to improve variant calling. However, large collections of variants for this purpose often are unavailable to research communities.
Ryan F McCormick, Sandra Truong, John E Mullet   +2 more
exaly   +3 more sources

SparkRA: Enabling Big Data Scalability for the GATK RNA-seq Pipeline with Apache Spark [PDF]

Genes, 2020
The rapid proliferation of low-cost RNA-seq data has resulted in a growing interest in RNA analysis techniques for various applications, ranging from identifying genotype–phenotype relationships to validating discoveries of other analysis results. However, many practical applications in this field are limited by the available computational resources ...
Zaid Al-Ars, Hamid Mushtaq
exaly   +5 more sources

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SW+: On Accelerating Smith-Waterman Execution of GATK HaplotypeCaller

Lecture Notes in Computer Science, 2020
Next Generation sequencing is widely used today in several applications such as in studying hereditary diseases or in prenatal genetic testing. Genome Analysis ToolKit (GATK) workflow is currently the best practice flow in use in industry and academia. Variant Calling, the last step in the GATK pipeline, is performed by GATK HaplotypeCaller.
Andreas Moshovos
exaly   +2 more sources