SEQUENCEDIVERSITY

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

LICENSE

Copyright 2011-2022 (C) Erik Garrison and vcflib contributors. MIT licensed.

AUTHORS

Erik Garrison and vcflib contributors.