PVST(1) pVst (VCF statistics) PVST(1)

pVst

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

pVst calculates vst, a measure of CNV stratification.

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

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vcflib(1)

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

Erik Garrison and vcflib contributors.

pVst (vcflib)