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

AUTHORS
Erik Garrison and vcflib contributors.