NAME

       sequenceDiversity

SYNOPSIS

       sequenceDiversity –target 0,1,2,3,4,5,6,7 –file my.vcf

DESCRIPTION

       The sequenceDiversity program calculates two popular metrics of haplotype diversity: pi and extended hap‐
       lotype homozygoisty (eHH).  Pi is calculated using the Nei and Li 1979 formulation.  eHH a convenient way
       to  think about haplotype diversity.  When eHH = 0 all haplotypes in the window are unique and when eHH =
       1 all haplotypes in the window are identical.

OPTIONS

              Output : 5 columns:
                       1.  seqid
                       2.  start of window
                       3.  end of window
                       4.  pi
                       5.  eHH

              required: t,target     -- argument: a zero base comma separated list of target individuals corresponding to VCF columns
              required: f,file       -- argument: a properly formatted phased VCF file
              required: y,type       -- argument: type of genotype likelihood: PL, GL or GP
              optional: a,af         -- sites less than af  are filtered out; default is 0
              optional: r,region     -- argument: a tabix compliant region : "seqid:0-100" or "seqid"
              optional: w,window     -- argument: the number of SNPs per window; default is 20

              Type: statistics

EXIT VALUES

       0      Success

       not 0  Failure

SEE ALSO

       vcflib(1)

OTHER

LICENSE

       Copyright 2011-2024 (C) Erik Garrison and vcflib contributors.  MIT licensed.   Copyright  2020-2024  (C)
       Pjotr Prins.

AUTHORS

       Erik Garrison and vcflib contributors.

sequenceDiversity (vcflib)                                                                  SEQUENCEDIVERSITY(1)