pVst(1) · carta

Usage

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