PVST(1) pVst (VCF statistics) PVST(1) NAME pVst SYNOPSIS pVst -target 0,1,2,3,4,5,6,7 -background 11,12,13,16,17,19,22 -file my.vcf -type CN DESCRIPTION pVst calculates vst, a measure of CNV stratification. OPTIONS The statistic Vst is used to test the difference in copy numbers at each SV between two groups: Vst = (Vt-Vs)/Vt, where Vt is the overall variance of copy number and Vs the average variance within populations. Output : 4 columns : 1. seqid 2. position 3. end 3. vst 4. probability required: t,target -- argument: a zero based comma separated list of target individuals corresponding to VCF columns required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns required: f,file -- argument: a properly formatted VCF. required: y,type -- argument: the genotype field with the copy number: e.g. CN|CNF optional: r,region -- argument: a tabix compliant genomic range : seqid or seqid:start-end optional: x,cpu -- argument: number of CPUs [1] optional: n,per -- argument: number of permutations [1000] 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. pVst (vcflib) PVST(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXIT VALUES | SEE ALSO | OTHER | LICENSE | AUTHORS
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