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

# sequenceDiversity(1)

## NAME

**sequenceDiversity**

## SYNOPSIS

**sequenceDiversity** –target 0,1,2,3,4,5,6,7 –file my.vcf

## DESCRIPTION

The **sequenceDiversity** 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.

## OPTIONS

-

  ```
  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 : "seqid:0-100" or "seqid"
  optional: w,window     -- argument: the number of SNPs per window; default is 20
  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.