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% PVST(1) pVst (vcflib) | pVst (VCF statistics)
% Erik Garrison and vcflib contributors
# NAME
**pVst**
# SYNOPSIS
**pVst** --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf --type CN
# DESCRIPTION
**pVst** calculates vst, a measure of CNV stratification.
# OPTIONS
```
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
```
# EXIT VALUES
**0**
: Success
**not 0**
: Failure
# SEE ALSO
[vcflib](./vcflib.md)(1)
# OTHER
## Source code
[pVst.cpp](https://github.com/vcflib/vcflib/blob/master/src/pVst.cpp)
# LICENSE
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
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