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SNP filtering - Coggle Diagram

- - - - Read or mapping quality
      - Read depth or coverage
    - - Missing data
      - MAF and MAC
- - - - can only work on single-sample vcfs
  - - - ExcessHet
    - - Filtering variants bcftools
        
        bcftools stats
        
        MONOALLELIC
- - - - There is a value called ExcHet. Can we just filter based on it?
        
        [Finished]Reading about fill-tag doc
        
        fill-tags based on populations instead of all samples (-S n1006_filltags.file). Then all tags filled were calculated at population level. Then I think we should do TS1 and TS3 instead of 081.081.
        
        Did not say how to filter based on ExcHet. Only said 1 is good and 0 is bad.
      - plinkQC
        
        Genotype quality control with plinkQC
        
        Ancestry check
        
        He
      - GATK can calculate something called ExcessHet , maybe can calculate and compare with ExcHet to see whether it is the same thing since this one is for sure P-value related.
        
        This assumes no consanguinity in the population, which is the same as HWE, therefore we also need to either calculate within each population, or only use founders. Actually when we use -S all the tags it filled are calculated for each population
      - Conclusion: no filtering for HWE and He for now.
    - - bcftools +fill-tags
        
        based on populations instead of all samples (-S)