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
OUTPUT
- Trait-increasing RAREFY scores and trait-decreasing RAREFY scores are saved in "sim1_simul_rarefy.trait.Decreasing.result" and "sim1_simul_rarefy.trait.Increasing.result" separately.
- Use the following command to sort the RAREFY score to select informative individuals:
sort -k7 -gr sim1_simul_rarefy.trait.Increasing.result | head -10
- The top 10 selected individuals are:
famid pid fatid motid sex residual rarefy_idv_score rarefy_fam_score 1994 5 1 2 1 4.05563 0.839037 2.73226 1994 2 0 0 2 3.66226 0.829384 2.73226 345 1 0 0 1 3.45514 0.785963 1.95526 345 4 1 2 2 3.20513 0.782924 1.95526 3503 4 1 2 2 3.33598 0.621358 1.85789 3503 1 0 0 1 2.15643 0.619741 1.85789 1994 3 1 2 1 2.25633 0.607197 2.73226 3503 5 1 2 1 2.51068 0.601241 1.85789 1994 4 1 2 2 1.85392 0.437127 2.73226 3860 2 0 0 2 2.45598 0.405228 1.5474