Man page - pvst(1)

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Manual

PVST

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
EXIT VALUES
SEE ALSO
OTHER
LICENSE
AUTHORS

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

OTHER

LICENSE

AUTHORS

Erik Garrison and vcflib contributors.