GWAS Simulation

comvert hmp to ped1, ped2, map file
SB1.ped, SB2.ped, SB.map

1, choose 20 markers for 30 times
(WD: /share/bioinfo/miaochenyong/GWAS/SB/20Markers-1To5Effect)
python ../choose_multi-markers.py SB.imputed.916.filtered.hmp 20 30 marker pheno

2, combine pheno, ped1, ped2 to intact ped file
python ../combinePed.py SB1.ped SB2.ped SB pheno 30

3, copy SB.map to 30 different SB-*.map
python CPmapTOmore.py

4, *map, *ped to *bed, *bim, *fam
python generatePLINKcmd.py > PLINK.cmd
chmod 777 PLINK.cmd
parallel -j 6 < PLINK.cmd

5, run gemma
python generateGemmaCmd.py > gemma.cmd
chmod 777 gemma.cmd
parallel -j 6 < gemma.cmd

Calculate FDR value:
(WD: /share/bioinfo/miaochenyong/GWAS/SB/20Markers-1To5Effect-FDR)
1, shuffle pheno1.txt to 100 pheno*.txt
python ../shufflePheno.py pheno3.txt 100 pheno-shuffled

2, combine pheno, ped1, ped2 to intact ped file
python ../combinePed.py SB1.ped SB2.ped SB-shuffle pheno-shuffled 100

3, copy SB.map to 10 different SB-shuffle*.map
python CPmapTOmore.py 100 SB-shuffle

4, *map, *ped to *bed, *bim, *fam
python ../generatePLINKcmd.py > PLINK.cmd
chmod 777 PLINK.cmd
parallel -j 10 < PLINK.cmd

5, run gemma
python ../generateGemmaCmd.py > gemma.cmd
chmod 777 gemma.cmd
parallel -j 10 < gemma.cmd

6, calsulate FDR
cd output
python ../../calculateFDR.py SB-shuffle- 100 results.txt

Calculate average Power:
(WD: /share/bioinfo/miaochenyong/GWAS/SB/20Markers-1To5Effect/output)
python ../../calPower.py SB- markers-new 30 /share/bioinfo/miaochenyong/GWAS/SB/20Markers-1To5Effect-FDR/output/results.txt SB-
python ../../calAveragePower.py

cmiao

UNL

beadle center