sequenceDiversity.md

% 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(1)

OTHER

Source code

sequenceDiversity.cpp

LICENSE

Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.