FindSV

FindSV is a bioinformatic tool to detect structural variants (SVs) from whole-genome sequencing (WGS) data. It was part of a pipeline used to analyze WGS data for identifying various types of genetic variants, including copy number variants (CNVs), single nucleotide variants (SNVs), and short tandem repeat (STR) expansions, in individuals with intellectual disability.

The tool was validated on a cohort with known CNVs and successfully detected all variants, including trisomies, deletions, and duplications ranging in size from 500 bp to 155 Mb. FindSV and other tools developed by the authors (SVDB, Rhocall, Rhoviz, and vcf2cytosure) were then applied to analyze WGS data from prospective cases referred for chromosomal microarray analysis (CMA).

Topic

Whole genome sequencing;DNA structural variation;DNA polymorphism;Pathology;Genotype and phenotype

Detail

  • Operation: Indel detection;Variant calling;Genotyping;Filtering

  • Software interface: Script,Workflow

  • Language: Shell,Python

  • License: Not stated

  • Cost: Free of charge

  • Version name: 1.0.0

  • Credit: SciLifeLab, Stockholm County Council, Swedish Research Council, Swedish Brain Foundation, The Hållsten Research Foundation, Karolinska Institutet, The Royal Physiographic Society in Lund, Knut and Alice Wallenberg Foundation.

  • Input: -

  • Output: -

  • Contact: Anna Lindstrand anna.lindstrand@ki.se

  • Collection: -

  • Maturity: -

Publications

  • From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability.
  • Lindstrand A, et al. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. 2019; 11:68. doi: 10.1186/s13073-019-0675-1
  • https://doi.org/10.1186/S13073-019-0675-1
  • PMID: 31694722
  • PMC: PMC6836550

Download and documentation

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