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.\" Automatically generated by Pandoc 2.7.3
.\"
.TH "PVST" "1" "" "pVst (vcflib)" "pVst (VCF statistics)"
.hy
.SH NAME
.PP
\f[B]pVst\f[R]
.SH SYNOPSIS
.PP
\f[B]pVst\f[R] \[en]target 0,1,2,3,4,5,6,7 \[en]background
11,12,13,16,17,19,22 \[en]file my.vcf \[en]type CN
.SH DESCRIPTION
.PP
\f[B]pVst\f[R] calculates vst, a measure of CNV stratification.
.SH OPTIONS
.IP
.nf
\f[C]
The statistic Vst is used to test the difference in copy numbers at
each SV between two groups: Vst = (Vt-Vs)/Vt, where Vt is the overall
variance of copy number and Vs the average variance within
populations.
Output : 4 columns :
1. seqid
2. position
3. end
3. vst
4. probability
required: t,target -- argument: a zero based comma separated list of target individuals corresponding to VCF columns
required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns
required: f,file -- argument: a properly formatted VCF.
required: y,type -- argument: the genotype field with the copy number: e.g. CN|CNF
optional: r,region -- argument: a tabix compliant genomic range : seqid or seqid:start-end
optional: x,cpu -- argument: number of CPUs [1]
optional: n,per -- argument: number of permutations [1000]
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.
|
