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% SEQUENCEDIVERSITY(1) sequenceDiversity (vcflib) | sequenceDiversity (VCF statistics)
% Erik Garrison and vcflib contributors
# 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](./vcflib.md)(1)
# OTHER
## Source code
[sequenceDiversity.cpp](https://github.com/vcflib/vcflib/blob/master/src/sequenceDiversity.cpp)
# LICENSE
Copyright 2011-2024 (C) Erik Garrison and vcflib contributors. MIT licensed.
Copyright 2020-2024 (C) Pjotr Prins.
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