pVst.md

% PVST(1) pVst (vcflib) | pVst (VCF statistics) % Erik Garrison and vcflib contributors

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

Source code

pVst.cpp

LICENSE

Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.