SMAP snp-seq

This is the manual for the component SMAP snp-seq of the SMAP package.

SMAP snp-seq was designed specifically to design HiPlex amplicon primers for targeted resequencing of polymorphic loci, while accounting for neighboring SNPs during primer design.

SMAP snp-seq requires a reference genome sequence, a list of SNPs that should be targetted by amplicon sequencing (target), a VCF file with all known SNPs (background), and a list of SNPs that can be used to create a customized reference sequence.

SMAP snp-seq creates a list of primer sequences, a FASTA file with the amplicon sequences, a GFF file with primer sequence coordinates, a BED file with SMAPs for downstream analysis with SMAP haplotype-sites or a GFF file with border coordinates for downstream analysis with SMAP haplotype-window.

Contents:

• Scope & Usage
  • Scope
  • Integration in the SMAP workflow
  • Guidelines for variant calling
  • Commands & options
  • Example commands
  • Output
• Feature Description
  • Reference
  • Template region
  • Target region
  • From Template region to Template sequence
  • Primer3 amplicon design
  • Output
• How It Works
  • overview of input, workflow, options, and output
  • Defining regions according to different scenario’s
• Examples
  • Illustration of amplicon distribution
• Recommendations & Troubleshooting
  • Recommendations
  • Troubleshooting