drop-mutations-into-pedigree Files

 REAL DATA
---------

1. In the case of the real data add generations of full sib mating
leading up to the progenitors:

$ add-inbred-line-progenitor.pl -infile C3H_ped_rekey_Jun2023_fixeff_1litvia.csv -outfile C3H_ped_rekey_Jun2023_fixeff_1litvia-extra-gens.csv -generations 20

2. Drop mutations into the pedigree

$ drop-mutations-into-ped C3H_ped_rekey_Jun2023_fixeff_1litvia-extra-gens.csv seedfile dropped-mutations.txt 1000000 1

3. Collate the mutations by generation and MA line

To calculate between line variance (mutation drop data):

$ collate-mutations.pl -infile dropped-mutations.txt -outfile junk.csv -muts -1 -V_M 0.01 -blv_mode

To calculate line means (mutation drop data):

$ collate-mutations.pl -infile dropped-mutations.txt -outfile junk.csv -muts -1 -V_M 0.01

4. Compute MA line means and between line variance from the phenotypic data:

$ compute_ma_line_means_blv.pl -infile C3H_ped_rekey_Jun2023_fixeff_1litvia-extra-gens.csv -outfile_mean ma-line-means-tail.csv -outfile_blv ma-line-blv-tail.csv -trait Tail

5. Compute average between line environmental variance for VE = 1

$ compute_mean_env_BLV.pl -infile C3H_ped_rekey_Jun2023_fixeff_1litvia-extra-gens.csv -outfile expected_BLV_VE_1.csv -seedfile seedfile -reps 100

6. Compute average between line genetic variance for VM = 1, single replicate

$ collate-mutations.pl -infile dropped-mutations.txt -outfile junk4.csv -muts -1 -V_M 1 -V_E 0.0 -blv_mode

7. Compute average between line genetic variance for VM = 1, average of 100 replicates

$ compute_mean_VG.pl -infile C3H_ped_rekey_Jun2023_fixeff_1litvia-extra-gens.csv -outfile expected_BLV_VM_1.csv -seedfile seedfile

8. Fit V_M and V_E by least squares:

$ estimate-vm-ve-from-blv expected_BLV_VE_1.csv expected_BLV_VM_1.csv ma-line-blv-tail.csv seedfile output_vm_ve.csv

9. Complete pipeline (including boostrap option):

$ pipeline.pl -infile C3H_ped_rekey_Jun2023_fixeff_1litvia-extra-gens.csv -outfile results-boot.csv -seedfile seedfile -nboot 100 -correct_fixed -asreml_effects_file ASREML-EFFECTS.csv

10. Rank Vm/Ve estimates:

$ compute-h2m-from-boot-output.pl -infile results-boot.csv-tail

SIMULATED DATA
--------------

1. Generate an MA line pedigree by simulation:

$ gen-ped.pl -pedfile junk.txt -cfile junk1.txt -gens 100 -ma_lines 100 -litsize 5


2. Drop mutations into the pedigree:

$ drop-mutations-into-ped junk.txt seedfile junk2.txt 100000 1


Compute average between line genetic variance for VM = 1, single replicate

$ collate-mutations.pl -infile junk2.txt -outfile junk4.csv -muts -1 -V_M 1 -V_E 0.0 -blv_mode