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2021 Action Plan - Coggle Diagram

- - - - Map WGS data
        
        Burrows-Wheeler Aligner (BWA)
        
        ID and analyze variants for pathogenicity
        
        modified computational pipeline developed by EGGL
        
        Broad Institute Genome Analysis Toolkit (GATK) best practices
        
        Indel realignment
        
        base-quality score recalibration
        
        Hard filtering for high variance
        
        Variant calling
        
        Genome Variant Call Format (genome VCFs)
        
        1 more item...
        
        GATK Haplotype Caller
        
        2 more items...
        
        BCFtools mpileup
  - - - Predict functional effects for each variant
        
        ANNOVAR
        
        SnpEff
        
        Use custom dictionaries based on the RefSeq version of each species-specific genomes.
  - - - descriptive statistics for all variant callers
        
        intersection will be created using BCFtools.
      - High impact variants will be extracted
- - - - decreased genetic burden compared to domesticated species