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Variant Calling: Methods and Protocols
Hardcover
Series: Methods in Molecular Biology, Book 2493
ISBN13: 9781071622926
Publisher: Humana Pr
Published: Jun 26 2022
Pages: 354
Weight: 1.88
Height: 0.81 Width: 7.00 Depth: 10.00
Language: English
1. Data Processing and Germline Variant Calling with the Sentieon pipeline
Rafael Aldana and Donald Freed
2. MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling
Shuangxi Ji, Matthew D. Montierth, and Wenyi Wang
3. Octopus: Genotyping and Haplotyping in Diverse Experimental Designs
Daniel P Cooke
4. Accurate Ensemble Prediction of Somatic Mutations with SMuRF2
Weitai Huang, Ngak Leng Sim, and Anders J Skanderup
5. Detecting Medium and Large Insertions and Deletions with Transindel
Ting-You Wang and Rendong Yang
6, DECoN: A detection and visualisation tool for exonic copy number variants
Anna Fowler
7. FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing
Arshi Arora, Ronglai Shen, and Venkatraman E. Seshan
8. Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms
Lixing Yang
9. Structural Variant Detection from Long-Read Sequencing Data with cuteSV
Tao Jiang, Shiqi Liu, Shuqi Cao, and Yadong Wang
10. Identifying Somatic Mitochondrial DNA Mutations
Jisong An, Kyoung Il Min, and Young Seok Ju
11. Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq data using SplAdder
Philipp Markolin, Gunnar Rätsch, and Andre Kahles
12. PipeIT: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data
Andrea Garofoli, Désirée Schnidrig, and Charlotte K Y Ng
13. Variant calling from RNA-seq data using the GATK joint genotyping workflow
Jean-Simon Brouard and Nathalie Bissonnette
14. UMI-Varcal: a low-frequency variant caller for UMI-tagged paired-end sequencing data
Vincent Sater, Pierre-Julien Viailly, Thierry Lecroq, Élise Prieur-Gaston, Élodie Bohers, Mathieu Viennot, Philippe Ruminy Hélène Dauchel, Pierre Vera, and Fabrice Jardin
15. Alignment-free genotyping of known variations with MALVA
Giulia Bernardini, Luca Denti, and Marco Previtali
16. Kmer2SNP: Reference-free heterozygous SNP calling using k-mer frequency distributions Yanbo Li, Hardip Patel, and Yu Lin
17. Somatic Single Nucleotide Variant Calling from Single Cell DNA sequencing data using SCAN-SNV
Sajedeh Bahonar and Hesam Montazeri
18. Copy Number Variation Detection by Single-Cell DNA sequencing with SCOPE
Rujin Wang and Yuchao Jiang
19. Variant Annotation and Functional Prediction: SnpEff
Pablo Cingolani
20. Annotating Cancer-Related Variants At Protein-Protein Interface with Structure-PPi Miguel Vazquez and Tirso Pons
21. Preanalytical Variables and Sample Quality Control For Clinical Variant Analysis Ilaria Alborelli and Philip M. Jermann
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