S6 MagicReconstruct

MagicReconstruct

The magicreconstruct performs haplotype reconstruction using the default HMM forward-backward algorithm (hmmalg = "forwardbackward"). The Viterbi algorithm (hmmalg = "viterbi") is also available.

# code for Julia
using MagicReconstruct
cd(@__DIR__)
genofile = outstem*"_magicimpute_geno.vcf.gz"
pedfile = outstem*"_magicfilter_ped.csv"
magicreconstruct(genofile,pedfile;        
    outstem     
)

# code for Linux shell. 
# For Window CMD, replace multiline key \ by  ^, and replace comment-key # by ::
julia rabbit_magicreconstruct.jl -g example_magicimpute_geno.vcf.gz \
    -p example_magicfilter_ped.csv \
    --nworker 5 \
    -o example

Output files

Output: plot #breakpoints

outstem*"_magicreconstruct_posterior_recom.png" is the Violin plot of the posterior distribution of the number of recombination breakpoints (per Morgan) among offspring. The x-axis denotes the prior number of recombination breakpoints. See outstem*"_magicreconstruct_posterior_recom.csv" for the exact results.

Output: plot inbredcoef

The output file outstem*"_magicreconstruct_inbredcoef.png" is the plot of the estimated inbreeding coefficients; the red dots denote the theoretical expectation. See the output file outstem*"_magicreconstruct_ancestry.csv.gz" for the exact results.

Output: plot condprob

The output file outstem*"_magicreconstruct_ancestry.csv.gz" saves the main results for the downstream QTL mapping. We can read the output file by MagicBase.readmagicancestry and visualize the conditional probability by MagicBase.plotcondprob. The output file outstem*"_magicreconstruct_probplots.tar" includes plots for up to 10 offspring per subpopulation.

using Plots
using MagicBase
magicancestry = readmagicancestry("example_magicreconstruct_ancestry.csv.gz")
truefgl = formmagicgeno("example_magicsimulate_truefgl.csv.gz","example_magicfilter_ped.csv");
MagicBase.plotcondprob(magicancestry;
    truefgl,
    offspring=250,
    probtype="diploprob",
    size = (850,350),
    left_margin = 5Plots.mm
)

The plot markers ("x") indicate the true origin states, and the bottom vertical bars ("|") indicate the marker positions.

MagicBase.plotcondprob(magicancestry;
    truefgl,
    offspring=250,
    probtype="genoprob",
    size = (850,250),
    left_margin = 5Plots.mm
)

MagicBase.plotcondprob(magicancestry;
    truefgl,
    offspring=250,
    probtype="haploprob",
    size = (850,250),
    left_margin = 5Plots.mm
)