RAREFY TUTORIAL
From Genome Analysis Wiki
Useful Wiki Pages
- The RAREFY Homepage
- The RAREFY Documentation
- The RAREFY COMMAND REFERENCE
- The FAQ
EXAMPLE DATA SET
- Please download the EXAMPLE file to your directory.
- In this example, 20,000 individuals in 4,000 nuclear families were simulated with 40% trait heritability.
- A variant with frequency 0.001 and effect size 2 SD was simulated in the sample. The variant was simulated to be trait-increasing.
COMMAND
- Use the following command to RAREFY the sample for both trait-increasing and trait-decreasing variants. Although this sample includes only trait-increasing variant, in real world, we do not know if the sample contains trait-increasing variants or trait-decreasing variants or both.
rarefy --ped sim1.ped --dat sim1.dat --inverseNormal --traitIncreasing --traitDecreasing --prefix sim1
