SMAP haplotype-window

This is the manual for the haplotype-window component of the SMAP package.

SMAP haplotype-window can extract haplotypes from HiPlex or Shotgun Sequencing reads mapped onto a reference sequence.

The scheme below shows the workflow combining either of two library preparation methods and/or sample types (individual genotyping or Pool-Seq).

Contents:

• Scope & Usage
  • Scope
  • Integration in the SMAP workflow
  • Commands & options
  • Example commands
  • Output
• Feature description
  • Haplotyping for different library preparation methods
  • Haplotyping for different sample types (individual or pool)
• How It Works
  • Workflow of SMAP haplotype-window
  • CRISPR/Cas extension of SMAP haplotype-window
• Recommendations & Troubleshooting
  • Recommendations
  • Troubleshooting