國立虎尾科技大學 |

Variant Calling = Methods and Protocols /

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Variant Calling/ edited by Charlotte Ng, Salvatore Piscuoglio.
Reminder of title:	Methods and Protocols /
other author:	Ng, Charlotte.
Description:	XI, 354 p. 57 illus., 44 illus. in color.online resource. :
Contained By:	Springer Nature eBook
Subject:	Genetics. -
Online resource:	https://doi.org/10.1007/978-1-0716-2293-3
ISBN:	9781071622933

Variant Calling = Methods and Protocols /
Variant CallingMethods and Protocols /[electronic resource] :edited by Charlotte Ng, Salvatore Piscuoglio. - 1st ed. 2022. - XI, 354 p. 57 illus., 44 illus. in color.online resource. - Methods in Molecular Biology,24931940-6029 ;. - Methods in Molecular Biology,2540.

Data Processing and Germline Variant Calling with the Sentieon pipeline -- MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling -- Octopus: Genotyping and Haplotyping in Diverse Experimental Designs -- Accurate Ensemble Prediction of Somatic Mutations with SMuRF2 -- Detecting Medium and Large Insertions and Deletions with Transindel -- DECoN: A detection and visualisation tool for exonic copy number variants -- FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing -- Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms -- Structural Variant Detection from Long-Read Sequencing Data with cuteSV -- Identifying Somatic Mitochondrial DNA Mutations -- Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq data using SplAdder -- PipeIT: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data -- Variant calling from RNA-seq data using the GATK joint genotyping workflow -- UMI-Varcal: a low-frequency variant caller for UMI-tagged paired-end sequencing data -- Alignment-free genotyping of known variations with MALVA -- Kmer2SNP: Reference-free heterozygous SNP calling using k-mer frequency distributions -- Somatic Single Nucleotide Variant Calling from Single Cell DNA sequencing data using SCAN-SNV -- Copy Number Variation Detection by Single-Cell DNA sequencing with SCOPE -- Variant Annotation and Functional Prediction: SnpEff -- Annotating Cancer-Related Variants At Protein-Protein Interface with Structure-PPi -- Preanalytical Variables and Sample Quality Control For Clinical Variant Analysis. .

This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls. Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field. .

ISBN: 9781071622933

Standard No.: 10.1007/978-1-0716-2293-3doiSubjects--Topical Terms:

578972
Genetics.

LC Class. No.: QH426-470

Dewey Class. No.: 576.5

Variant Calling = Methods and Protocols /
LDR:03931nam a22003855i 4500 001 1087768
003 DE-He213
005 20220625131044.0
007 cr nn 008mamaa
008 221228s2022 xxu| s |||| 0|eng d
020 $a 9781071622933 $9 978-1-0716-2293-3
024 7 $a 10.1007/978-1-0716-2293-3 $2 doi
035 $a 978-1-0716-2293-3
050 4 $a QH426-470
072 7 $a PSAK $2 bicssc
072 7 $a SCI029000 $2 bisacsh
072 7 $a PSAK $2 thema
082 0 4 $a 576.5 $2 23
245 1 0 $a Variant Calling $h [electronic resource] : $b Methods and Protocols / $c edited by Charlotte Ng, Salvatore Piscuoglio.
250 $a 1st ed. 2022.
264 1 $a New York, NY : $b Springer US : $b Imprint: Humana, $c 2022.
300 $a XI, 354 p. 57 illus., 44 illus. in color. $b online resource.
336 $a text $b txt $2 rdacontent
337 $a computer $b c $2 rdamedia
338 $a online resource $b cr $2 rdacarrier
347 $a text file $b PDF $2 rda
490 1 $a Methods in Molecular Biology, $x 1940-6029 ; $v 2493
505 0 $a Data Processing and Germline Variant Calling with the Sentieon pipeline -- MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling -- Octopus: Genotyping and Haplotyping in Diverse Experimental Designs -- Accurate Ensemble Prediction of Somatic Mutations with SMuRF2 -- Detecting Medium and Large Insertions and Deletions with Transindel -- DECoN: A detection and visualisation tool for exonic copy number variants -- FACETS: Fraction and Allele-Specific Copy Number Estimates from Tumor Sequencing -- Meerkat: An Algorithm to Reliably Identify Structural Variations and Predict Their Forming Mechanisms -- Structural Variant Detection from Long-Read Sequencing Data with cuteSV -- Identifying Somatic Mitochondrial DNA Mutations -- Identification, Quantification, and Testing of Alternative Splicing Events from RNA-Seq data using SplAdder -- PipeIT: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data -- Variant calling from RNA-seq data using the GATK joint genotyping workflow -- UMI-Varcal: a low-frequency variant caller for UMI-tagged paired-end sequencing data -- Alignment-free genotyping of known variations with MALVA -- Kmer2SNP: Reference-free heterozygous SNP calling using k-mer frequency distributions -- Somatic Single Nucleotide Variant Calling from Single Cell DNA sequencing data using SCAN-SNV -- Copy Number Variation Detection by Single-Cell DNA sequencing with SCOPE -- Variant Annotation and Functional Prediction: SnpEff -- Annotating Cancer-Related Variants At Protein-Protein Interface with Structure-PPi -- Preanalytical Variables and Sample Quality Control For Clinical Variant Analysis. .
520 $a This volume provides practical guidance on a variety of techniques and steps to ensure successful variant calling. Chapters detail methods for variant calling from single-nucleotide variants to structural variants, variant calling in specialized data types such as RNA-seq and UMI-tagged sequencing, alignment-free genotyping and SNP calling, variant detection in single-cell DNA sequencing data, variant annotation, and preanalytical quality control to ensure successful variant calling. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists step-by-step protocol to execute the algorithms, describes the input and output data, and includes tips on troubleshooting and known pitfalls. Authoritative and cutting-edge, Variant Calling: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field. .
650 0 $a Genetics. $3 578972
650 0 $a Bioinformatics. $3 583857
700 1 $a Ng, Charlotte. $e editor. $4 edt $4 http://id.loc.gov/vocabulary/relators/edt $3 1394843
700 1 $a Piscuoglio, Salvatore. $e editor. $4 edt $4 http://id.loc.gov/vocabulary/relators/edt $3 1394844
710 2 $a SpringerLink (Online service) $3 593884
773 0 $t Springer Nature eBook
776 0 8 $i Printed edition: $z 9781071622926
776 0 8 $i Printed edition: $z 9781071622940
776 0 8 $i Printed edition: $z 9781071622957
830 0 $a Methods in Molecular Biology, $x 1940-6029 ; $v 2540 $3 1387604
856 4 0 $u https://doi.org/10.1007/978-1-0716-2293-3
912 $a ZDB-2-PRO
950 $a Springer Protocols (Springer-12345)