SMAP delineate
This is the manual for the component SMAP delineate of the SMAP package.
SMAP delineate was designed specifically to analyze Stacks of GBS reads mapped onto a reference sequence. It is not meant for other types of NGS libraries.
SMAP delineate requires special preprocessing of GBS reads before read mapping. Please use instructions and software for GBS read preprocessing as described in the manual of GBprocesS.
Conversely, SMAP delineate may be used to analyze whether all preprocessing steps have been performed correctly, and to recognize and remove technical artefacts before downstream analysis of BAM files.
SMAP delineate analyzes read mapping distribution, and captures read mapping polymorphisms within loci and across samples.
To exploit read mapping polymorphisms as novel type of genetic diversity markers, SMAP delineate introduces the new concepts of Stack Mapping Anchor Points (SMAPs), Stacks, StackClusters and MergedClusters. Detailed information on these features can be found in the section Feature Description.
Contents:
- Scope & Usage
- Feature Description
- Definition of SMAPs, Stacks, StackClusters, and MergedClusters
- Why polymorphisms (SNPs and InDels) give rise to variation in mapping positions of reads
- Why Stacks exist in GBS data
- Polymorphisms at restriction enzyme sites affect GBS library construction
- Polymorphisms affect the effective sequenced region
- Polymorphisms affect read mapping
- SMAPs in separately mapped reads versus merged reads
- Retaining only the central region of loci
- How It Works
- Examples
- Recommendations & Troubleshooting