---
name: "pVst"
section: "1"
platform: "linux"
package: "libvcflib-tools"
version: "1.0.12+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pVst"
---

# pVst(1)

## 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**(1)](/vcflib/1.md)

## OTHER

## LICENSE

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

## AUTHORS

Erik Garrison and vcflib contributors.