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; Local Realignment Filter
 
; Local Realignment Filter
: Consider removing single nucleotide variants at sites where local realignment of all covering sequence reads suggests that a short indel polymorphism is present in the population.
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: Consider removing single nucleotide variants at sites where local realignment of all covering sequence reads suggests that a length polymorphism is present in the population.
    
; Read Depth
 
; Read Depth
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