Hi Guys! I work with genomic analysis of cattle. In my current project will make a Gene Network Analysis Associated with Quality Meat, starting a new systems biology approach called the Association Weight Matrix (AWM). Therefore, initially will need to perform a GWAS chip data 770k. Need one GWAS package that provides OUTPUT: p-value and additive genetic effect. Someone already has experience and can give any suggestions on what best software will adjust in my analysis? Some papers indicating the use of Qxpak5, but I did not adapt with this package. Thank U.
Dear Carlos
Most of the GWAS tools aid through R packages like GenABEL or a few from MATLAB. Did you try the Open source GenABEL?
Second, the additive, epistatic, QTL effects can be done with any normal statistical tools followed by Bonferroni correction and further proceeding to pathway analysis for your association studies. what you need to start is the GWAS analysis. Please try the one.
Best
Prash
Carlos,
After you analyzed the GWAS and got your odds ratios you can calculate the additive genetic effect by multiplying odds ratios for each variant that present in a genome and take the natural log of the product (check the literature for "polygenic risk score" - that has been done for psychiatric diseases for example and is the equivalent to what you probably call "breeding value"). To avoid overfitting you may want to split your data set first, so that you can test how well the polygenic risk score performs in an independent sample.
Anna
In our GWAS analysis, imputation and meta-analysis we use the SNPTEST package as a regular basis, it can output additive, dominant, recessive and heterogyzous effects in the association analysis. It also gives the effect size of the association (betas or Odds ratio). Is very easy to use and it is ment for large GWAS chips. Hope this helps.
Yes, you can read the documentation here: https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html
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