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