شناسایی واریانت ها- روشها و پروتکل ها Variant Calling_ Methods and Protocols

فهرست مطالب: Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix 1 Data Processing and Germline Variant Calling with the Sentieon Pipeline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Rafael Aldana and Donald Freed 2 MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 Shuangxi Ji, Matthew D. Montierth, and Wenyi Wang 3 Octopus: Genotyping and Haplotyping in Diverse Experimental Designs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 Daniel P. Cooke 4 Accurate Ensemble Prediction of Somatic Mutations with SMuRF2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Weitai Huang, Ngak Leng Sim, and Anders J. Skanderup 5 Detecting Medium and Large Insertions and Deletions with transIndel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67 Ting-You Wang and Rendong Yang 6 DECoN: A Detection and Visualization Tool for Exonic Copy Number Variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 Anna Fowler 7 FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Arshi Arora, Ronglai Shen, and Venkatraman E. Seshan 8 Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Lixing Yang 9 Structural Variant Detection from Long-Read Sequencing Data with cuteSV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 Tao Jiang, Shiqi Liu, Shuqi Cao, and Yadong Wang 10 Identifying Somatic Mitochondrial DNA Mutations . . . . . . . . . . . . . . . . . . . . . . . . 153 Jisong An, Kyoung Il Min, and Young Seok Ju 11 Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq Data Using SplAdder . . . . . . . . . . . . . . . . . . . . . . . 167 Philipp Markolin, Gunnar Ratsch, and Andre € ´ Kahles 12 PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 Andrea Garofoli, De´sire´e Schnidrig, and Charlotte K. Y. Ng 13 Variant Calling from RNA-seq Data Using the GATK Joint Genotyping Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205 Jean-Simon Brouard and Nathalie Bissonnette vii 14 UMI-Varcal: A Low-Frequency Variant Caller for UMI-Tagged Paired-End Sequencing Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235 Vincent Sater, Pierre-Julien Viailly, Thierry Lecroq, E´ lise Prieur-Gaston, E´ lodie Bohers, Mathieu Viennot, Philippe Ruminy, He´le`ne Dauchel, Pierre Vera, and Fabrice Jardin 15 Alignment-Free Genotyping of Known Variations with MALVA . . . . . . . . . . . . . . 247 Giulia Bernardini, Luca Denti, and Marco Previtali 16 Kmer2SNP: Reference-Free Heterozygous SNP Calling Using k-mer Frequency Distributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257 Yanbo Li, Hardip Patel, and Yu Lin 17 Somatic Single-Nucleotide Variant Calling from Single-Cell DNA Sequencing Data Using SCAN-SNV. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267 Sajedeh Bahonar and Hesam Montazeri 18 Copy Number Variation Detection by Single-Cell DNA Sequencing with SCOPE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279 Rujin Wang and Yuchao Jiang 19 Variant Annotation and Functional Prediction: SnpEff . . . . . . . . . . . . . . . . . . . . . . 289 Pablo Cingolani 20 Annotating Cancer-Related Variants at Protein–Protein Interface with Structure-PPi. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315 Miguel Vazquez and Tirso Pons 21 Preanalytical Variables and Sample Quality Control for Clinical Variant Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331 Ilaria Alborelli and Philip M. Jermann Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353   مشخصات فایل
عنوان (Title):	Variant Calling_ Methods and Protocols
نام فایل (File name):	917-www.GeneProtocols.ir-Variant Calling_ Methods and Protocols-Humana Press (2022).pdf
عنوان فارسی (Title in Persian):	شناسایی واریانت ها- روشها و پروتکل ها
ایجاد کننده:	Charlotte Ng, Salvatore Piscuoglio
زبان (Language):	انگلیسی English
سال انتشار:	2022
شابک ISBN:	1071622927, 9781071622926
نوع سند (Doc. type):	کتاب
فرمت (File extention):	PDF
حجم فایل (File size):	8.14 مگابایت
تعداد صفحات (Book length in pages):	352

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