BcfBreeder

Quick Start

BcfBreeder simulate offspring genomes based on given parental genomes.
INPUT:

• a pedigree in PLINK's format
• a phased bcf/vcf containing the founders of the pedigree
• recombination maps

OUTPUT:

• a phased bcf/vcf containing the genomes of founders and offspring
• (optional: if you add --recvalid <PATH_TO_VALIDATION> all the recombination sites will be written into <PATH_TO_VALIDATION>. I made this option for the validation of the method.)

To run BcfBreeder use the following command:
./bin/toy --vcf <PATH_TO_INPUT_VCF> --region <CHROMOSOME> --output <OUTPUT_VCF_PATH> --map <PATH_TO_RECOMBINATION_MAP> --ped <PATH_TO_PEDIGREE> --seed <SEED_TO_SET_RANDOMNESS>

You can run an example with the following command:
./bin/toy --vcf example/founders_genomes.bcf --region 22 --output example/simulated_genomes.bcf --map maps/genetic_maps.b37/chr22.b37.gmap.gz --ped example/pedigree.ped --seed 13524

Acknowaledgment

Most of the source code is based on code written by @odelaneau and @srubinacci in GLIMPSE.