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SEQUENCEDIVERSITY(1) sequenceDiversity (VCF statistics) 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 haplo- type 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 2011-2025 (C) Erik Garrison and vcflib contributors. MIT li- censed. Copyright 2020-2025 (C) Pjotr Prins. AUTHORS Erik Garrison and vcflib contributors. sequenceDiversity (vcflib) SEQUENCEDIVERSITY(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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