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020 _a9781071622933
_9978-1-0716-2293-3
024 7 _a10.1007/978-1-0716-2293-3
_2doi
050 4 _aQH426-470
072 7 _aPSAK
_2bicssc
072 7 _aSCI029000
_2bisacsh
072 7 _aPSAK
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082 0 4 _a576.5
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245 1 0 _aVariant Calling
_h[electronic resource] :
_bMethods and Protocols /
_cedited by Charlotte Ng, Salvatore Piscuoglio.
250 _a1st ed. 2022.
264 1 _aNew York, NY :
_bSpringer US :
_bImprint: Humana,
_c2022.
300 _aXI, 354 p. 57 illus., 44 illus. in color.
_bonline resource.
336 _atext
_btxt
_2rdacontent
337 _acomputer
_bc
_2rdamedia
338 _aonline resource
_bcr
_2rdacarrier
347 _atext file
_bPDF
_2rda
490 1 _aMethods in Molecular Biology,
_x1940-6029 ;
_v2493
505 0 _aData 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 _aThis 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 _aGenetics.
650 0 _aBioinformatics.
650 1 4 _aGenetics.
650 2 4 _aBioinformatics.
700 1 _aNg, Charlotte.
_eeditor.
_0(orcid)0000-0002-6100-0026
_1https://orcid.org/0000-0002-6100-0026
_4edt
_4http://id.loc.gov/vocabulary/relators/edt
700 1 _aPiscuoglio, Salvatore.
_eeditor.
_4edt
_4http://id.loc.gov/vocabulary/relators/edt
710 2 _aSpringerLink (Online service)
773 0 _tSpringer Nature eBook
776 0 8 _iPrinted edition:
_z9781071622926
776 0 8 _iPrinted edition:
_z9781071622940
776 0 8 _iPrinted edition:
_z9781071622957
830 0 _aMethods in Molecular Biology,
_x1940-6029 ;
_v2493
856 4 0 _uhttps://doi.org/10.1007/978-1-0716-2293-3
912 _aZDB-2-PRO
999 _c5646
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