.\" Automatically generated by Pandoc 2.14.0.3
.\"
.TH "SEQUENCEDIVERSITY" "1" "" "sequenceDiversity (vcflib)" "sequenceDiversity (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]sequenceDiversity\f[R]
.SH SYNOPSIS
.PP
\f[B]sequenceDiversity\f[R] \[en]target 0,1,2,3,4,5,6,7 \[en]file my.vcf
.SH DESCRIPTION
.PP
The \f[B]sequenceDiversity\f[R] 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.
.SH OPTIONS
.IP
.nf
\f[C]

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 : \[dq]seqid:0-100\[dq] or \[dq]seqid\[dq]                                    
optional: w,window     -- argument: the number of SNPs per window; default is 20                                               

Type: statistics


\f[R]
.fi
.SH EXIT VALUES
.TP
\f[B]0\f[R]
Success
.TP
\f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.