writeVCFOfSimulation: Write out VCF of simulated individual

In JesseGarcia562/psmc2msprime:

Description

Uses msprime and the reticulate package to write out a VCF to the simulated indidividual

Usage

writeVCFOfSimulation(simulation, outpath, ploidy = 2)

Arguments

simulation	An <msprime.trees.TreeSequence> object
outpath	The desired output path for the VCF you are trying to create.
ploidy	An integer that defines the ploidy of the individual you simulated. The default is 2, referring to diploid.

Value

Returns nothing. But writes a VCF file to the given outpath

Examples

msmcInference<-readMSMCInference(pathOfMSMCOutFinal = "../data/msprimeMultiHetSep/simulatedMsprime.oak.msmc.out.final.txt", mutationRate = 1e-8)
populationParametersChange<-generatePopulationParameterChanges(msmcInference)
generateMSPrimeFunction( outPath = "../code/msmc2msprime_Feb1.py", PopulationParametersChangeInput=populationParametersChange)
source_python("../code/msmc2msprime_Feb1.py")
simulation<-msmc_model(length=3e5, seed=30, mu=1.01e-08)
writeVCFOfSimulation(simulation, outpath = "../data/msprimeQLob.vcf", ploidy=2)

JesseGarcia562/psmc2msprime documentation built on May 29, 2019, 8:20 p.m.