granite

granite is a collection of software to work with genomic variants. The suite provides inheritance mode callers and utilities to filter and refine variants called by other methods in VCF format.

Contents:

• Install
• File Formats
  • ReadCountKeeper (.rck)
  • BinaryIndexGenome (.big)
  • Pedigree in JSON format
• Inheritance Mode Callers
  • novoCaller
  • comHet
• Variant Filtering
  • whiteList
  • blackList
  • cleanVCF
  • geneList
• Quality Check
  • qcVCF
  • validateVCF
  • SVqcVCF
• Utilities
  • mpileupCounts
  • toBig
  • rckTar
• VCF Parser
  • Import the library
  • Usage