pVst

       Erik Garrison and vcflib contributors.

pVst (vcflib)                                                                                            PVST(1)

pVst calculates vst, a measure of CNV stratification.

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       Copyright  2011-2024  (C)  Erik Garrison and vcflib contributors.  MIT licensed.  Copyright 2020-2024 (C)
       Pjotr Prins.

pVst

              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

vcflib(1)

pVst –target 0,1,2,3,4,5,6,7 –background 11,12,13,16,17,19,22 –file my.vcf –type CN