Suppose I received 5000 case and 5000 control GWAS study (suppose it is exom-array), what kinds of analysis I can conducted to make full use of the genetic data? According to my current knowledge, It looks I need to do it like the following way and I hope to get some suggestion to make the analysis perfect:
transfer exom-array plink format to VCF format
transfer all the probes to Forward chain.
PCA to remove population outlier
send it to Michigan Imputation Server to do imputation and phasing
do the statistic analysis with allele-base, genotype based- with different model: dominant, recessive and so on
do compound hetero-zygote scanning, do epistasis test, do interaction test...
do gene-based, pathway based analysis
do genetic risk score associated analysis
do biological validation
Any more suggestions??
- weighted burden tests