This tutorial covers simulation for DNA sequence data under
Proportion of synonymous and proportion of protective variants can be customized. Note that specification of selection coefficients have to be adjusted accordingly. Other common parameters are set as follows for all commands in this tutorial:
lenI=1800 # would like 1800, 5000, 10000 lenII=1800 fn="1800" reps=200
Boyko 2008 European population model, 37% synonymous variants:
spower simulate --regRange=[$lenI,$lenII] --fileName="Boyko2008European$fn" --numReps=$reps --N=[7947,7947,262,7019,7019,52907,52907] --G=[5000,84,1,5217,1,576] --mutationModel='finite_sites' --mu=1.8e-08 --selModel='multiplicative' --selDist='Boyko_2008_European' --steps=[100] --verbose=0 --revertFixedSites=False > Boyko2008European$fn.log
Boyko 2008 African population model, 37% synonymous variants:
spower simulate --regRange=[$lenI,$lenII] --fileName="Boyko2008African$fn" --numReps=$reps --N=[7778,7778,25636,25636] --G=[5000,1,6809] --mutationModel='finite_sites' --mu=1.8e-08 --selModel='multiplicative' --selDist='Boyko_2008_African' --steps=[100] --verbose=0 --revertFixedSites=False > Boyko2008African$fn.log
Scott H. Williamson 2005 NIEHS SNPs data and Adam Eyre-Walker 2006 Environmental Genome Project (EGP) data:
spower simulate --regRange=[$lenI,$lenII] --fileName="Eyre2006Williamson$fn" --numReps=$reps --N=[8211,8211,51340,51340] --G=[5000,1,908] --mutationModel='finite_sites' --mu=1.8e-08 --selModel='multiplicative' --selDist='Eyre-Walker_2006' --steps=[100] --verbose=0 --revertFixedSites=False > Eyre2006Williamson$fn.log
Kryukov 2009 European population model, 37% synonymous variants:
spower simulate --regRange=[$lenI,$lenII] --fileName="Kryukov2009European$fn" --numReps=$reps --N=[8100,8100,7900,900000] --G=[5000,10,370] --mutationModel='finite_sites' --mu=1.8e-08 --selModel='multiplicative' --selDist='Kyrukov_2009_European' --steps=[100] --verbose=0 --revertFixedSites=False > Kryukov2009European$fn.log
Different proportions of protective and detrimental variants, 20% protective, 43% deleterious and 37% non-synonymous:
spower simulate --regRange=[$lenI,$lenII] --fileName="Kryukov2009EuropeanProtective$fn" --numReps=$reps --N=[8100,8100,7900,900000] --G=[5000,10,370] --mutationModel='finite_sites' --mu=1.8e-08 --selModel='multiplicative' --selDist='mixed_gamma' --selCoef=[0.37,0.0,0.43,0.184,0.320,0.184,0.320,0.5] --steps=[100] --verbose=0 --revertFixedSites=False > Kryukov2009EuropeanProtective$fn.log
The resulting default output are *.sfs
and *.gdat
files in the input format compatible with SEQPower power analysis commands.