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.\" Automatically generated by Pandoc 2.7.3
.\"
.TH "SEGMENTFST" "1" "" "segmentFst (vcflib)" "segmentFst (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]segmentFst\f[R]
.SH SYNOPSIS
.PP
\f[B]segmentFst\f[R] -s 0.7 -f wcFst.output.txt
.SH DESCRIPTION
.PP
\f[B]segmentFst\f[R] creates genomic segments (bed file) for regions
with high wcFst
.SH OPTIONS
.IP
.nf
\f[C]
**segmentFst** provides a way to find continious regions with high Fst values. It takes the output of wcFst and produces a BED file. These high Fst region can be permutated with \[aq]permuteGPATwindow\[aq]
Output : 8 columns :
1. Seqid
2. Start (zero based)
3. End (zero based)
4. Average Fst
5. Average high Fst (Fst > -s)
6. N Fst values in segment
7. N high fst values in segment
8. Segment length
required: -f -- Output from wcFst
optional: -s -- High Fst cutoff [0.8]
Type: statistics
\f[R]
.fi
.SH EXIT VALUES
.TP
.B \f[B]0\f[R]
Success
.TP
.B \f[B]not 0\f[R]
Failure
.SH SEE ALSO
.PP
\f[B]vcflib\f[R](1)
.SH OTHER
.SH LICENSE
.PP
Copyright 2011-2020 (C) Erik Garrison and vcflib contributors.
MIT licensed.
.SH AUTHORS
Erik Garrison and vcflib contributors.
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