Welcome to intansv!

Integrative analysis of structural variations

This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visualization of structural variations are also implemented in the package.

intansv integrates the SV predictions of the following programs

• BreakDancer
• Pindel
• DELLY
• SVseq2
• CNVnator
• Lumpy
• SoftSearch

Install

• the latest development version from Github with

  install.packages("devtools")
  devtools::install_github("venyao/intansv")
  

• the latest development version from Bioconductor with

  if (!requireNamespace("BiocManager", quietly = TRUE))
      install.packages("BiocManager")
  BiocManager::install(version='devel')
  BiocManager::install("intansv")
  

Source code in GitHub

https://github.com/venyao/intansv

Help Manual

Overview of intansv

intansv development version 1.27.0 support the following version of SV prediction programs

• BreakDancer version 1.4.5, example output
• Pindel version v0.2.5b9, example output
• DELLY version 0.8.1, example output
• SVseq2 version 2.2, example output
• CNVnator version 0.3.3, example output
• Lumpy version 0.3.0, example output
• SoftSearch version 2.4, example output

intansv development version 1.21.0 support the following version of SV prediction programs

• BreakDancer version 1.4.5, example output
• Pindel version v0.2.5b9, example output
• DELLY version 0.7.6, example output
• SVseq2 version 2.2, example output
• CNVnator version 0.3.3, example output
• Lumpy version 0.2.13, example output
• SoftSearch version 2.4, example output

intansv development version 1.17.1 support the following version of SV prediction programs

• BreakDancer version 1.4.5, example output
• Pindel version v0.2.5b9, example output
• DELLY version 0.7.6, example output
• SVseq2 version 2.2, example output
• CNVnator version 0.3.3, example output
• Lumpy version 0.2.13, example output
• SoftSearch version 2.4, example output

intansv release version 1.7.3 support the following version of SV prediction programs

• BreakDancer version 1.4.5, example output
• Pindel version 0.2.5a8, example output
• DELLY version 0.6.1, example output
• SVseq2 version 2.2, example output
• CNVnator version 0.3, example output
• Lumpy version 0.2.8, example output
• SoftSearch version 2.4, example output

intansv release version 1.7.1 support the following version of SV prediction programs

• BreakDancer version 1.0r112, example output
• Pindel version 0.2.4t, example output
• DELLY version 0.0.11, example output
• SVseq2 version 2.2, example output
• CNVnator version 0.2.7, example output
• Lumpy version 0.1.5, example output
• SoftSearch version 2.3, example output

Available Genome Annotation files storaged as ‘Rdata’ created from Gff3 files

• evidence-based annotation of the human genome (GRCh38), version 22 (Ensembl 79)
• evidence-based annotation of the human genome (GRCh37), version 19 (Ensembl 74)
• annotation of the human genome (GRCh38.p7) provided by GENCODE, Release 25

Report bugs

If you find any bugs using intansv, please create an issue or send me an email.

Contact information

ywhzau at gmail.com