S3 MagicCall

Genotype calling

The magiccall performs genotype calling marker by marker. It first estimates founder genotypes and likelihood parameters including sequence allelic balance bias and overdispersion, and then calculates posterior genotype probabilities for offspring. magiccall is necessary only for sequence data.

# code for Julia
using Distributed # set up parallel computation 
nprocs() < 6 && addprocs(6-nprocs())
@everywhere using MagicCall  
using MagicCall  
cd(@__DIR__)     
genofile = outstem*"_magicfilter_geno.vcf.gz"
pedfile = outstem*"_magicfilter_ped.csv"
magiccall(genofile,pedfile;    
    outstem
)

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

Output files

Output: genotyping error

outstem*"_magiccall_inferred_error.png" gives the statistical plots of inferred error rates among markers. Note that error rates were estimated independently among markers.