1% PVST(1) pVst (vcflib) | pVst (VCF statistics) 2% Erik Garrison and vcflib contributors 3 4# NAME 5 6**pVst** 7 8# SYNOPSIS 9 10**pVst** --target 0,1,2,3,4,5,6,7 --background 11,12,13,16,17,19,22 --file my.vcf --type CN 11 12# DESCRIPTION 13 14**pVst** calculates vst, a measure of CNV stratification. 15 16 17 18# OPTIONS 19 20``` 21 22 23 24 25The statistic Vst is used to test the difference in copy numbers at 26each SV between two groups: Vst = (Vt-Vs)/Vt, where Vt is the overall 27variance of copy number and Vs the average variance within 28populations. 29 30Output : 4 columns : 31 1. seqid 32 2. position 33 3. end 34 3. vst 35 4. probability 36 37required: t,target -- argument: a zero based comma separated list of target individuals corresponding to VCF columns 38required: b,background -- argument: a zero based comma separated list of background individuals corresponding to VCF columns 39required: f,file -- argument: a properly formatted VCF. 40required: y,type -- argument: the genotype field with the copy number: e.g. CN|CNF 41optional: r,region -- argument: a tabix compliant genomic range : seqid or seqid:start-end 42optional: x,cpu -- argument: number of CPUs [1] 43optional: n,per -- argument: number of permutations [1000] 44 45Type: statistics 46 47 48 49``` 50 51 52 53 54 55# EXIT VALUES 56 57**0** 58: Success 59 60**not 0** 61: Failure 62 63# SEE ALSO 64 65 66 67[vcflib](./vcflib.md)(1) 68 69 70 71# OTHER 72 73## Source code 74 75[pVst.cpp](https://github.com/vcflib/vcflib/blob/master/src/pVst.cpp) 76 77# LICENSE 78 79Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed. 80 81<!-- 82 Created with ./scripts/bin2md.rb scripts/bin2md-template.erb 83--> 84