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SMAP delineate
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SMAP target-selection
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SMAP grm
Scope & Usage
Feature Description
How It Works
Examples
Recommendations & Troubleshooting
SMAP
SMAP grm
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SMAP grm
This is the manual for the component
SMAP grm
of the SMAP package.
SMAP grm
was designed to create genetic relationship matrices (grm) based on multi-allelic haplotypes generated by
SMAP haplotype-sites
or
SMAP haplotype-window
.
Contents:
Scope & Usage
Scope
Integration in the SMAP workflow
Example input files
Commands & options
Example commands
Output
Feature Description
Setting the stage
Jaccard Distance
Information content of loci with Shared or Unique haplotypes
Loci with Complete Unique haplotypes
Loci with Partial Unique haplotypes
Loci with Complete Shared haplotypes
Loci with Partial Shared haplotypes
How It Works
Sample selection, sample names, and sample order
Locus selection
Filtering for locus completeness
Filtering for sample completeness
Plot line curves
Estimate pairwise genetic similarities and distances
Calculate the locus information content
References
Examples
Illustration
Recommendations & Troubleshooting
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