SMAP sliding-frames

This is the manual for the SMAP sliding-frames module of the SMAP package.

The first step prior to running SMAP haplotype-sites is the definition of the locus start and end points.

The module SMAP sliding-frames should be used to define sliding frames covering SNPs and/or structural variants in Shotgun data.

The module SMAP delineate should be run for GBS data to define relevant loci and read mapping polymorphisms in a data-driven manner.

The module SMAP design should be used for integrated design of HiPlex PCR primers and downstream analysis with SMAP haplotype-sites and/or SMAP haplotype-window.

Contents:

• Scope & Usage
  • Scope
  • Integration in the SMAP workflow
  • Required input
  • Commands & options
  • Example commands
  • Output
• Feature Description
• How It Works
  • Haplotyping sliding frames with adjacent SNPs
  • Haplotyping the junction sites of large structural variants such as deletions and inversions
• Examples
  • Illustration
• Recommendations & Troubleshooting