computePiPerCallableSites: 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

computePiPerCallableSites(msprimeVCFPath, windowSize = 5e+05,
  totalGenomeLength)

Arguments

msprimeVCFPath	Path to the msprime generated VCF
windowSize	Window size used to compute pi.
totalGenomeLength	Total genome length simulated.

Value

Returns the windowed piPerCallableSites for a simulated individual.

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)
generateMultiHetSep(msprimeVCF = "../data/msprimeQLob.vcf",outpath = "../data/msprimeQLob_multihetsep.txt")

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