Man page - sequencediversity(1)

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Manual

SEQUENCEDIVERSITY

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

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 haplotype 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

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.