MafFilter Manual 1.3.1: DiversityStatistics

2.3.1.11 Sequence diversity statistics

DiversityStatistics computes sequence diversity statistics, including:

Number of segregating sites,
Watterson’s theta.
Tajima’s pi (average pairwise dissimilarity).
Tajima’s D.

Synopsis:

maf.filter=                                   \
    [...],                                   
    SequenceStatistics(                       \
        statistics=(\                         \
            [...],                                                    
            DiversityStatistics(              \
                ingroup=(samp1,samp2,samp3)), \
            [...]),                           \
        ref_species=samp1,                    \
        file=data.statistics.csv),            \
    [...]

Arguments:

ingroup={list}: A list of sequences to be considered in the statistics calculations.