vartools - Variant Association tools R-package

vartools offers ten varitant association tests:

• CMC: Combined and Multivariate Collapsing Method for Rare Variants
• KBAC: Kernel Based Adaptive Clustering Method
• RBT: Replication Based Test for Protective Variants
• VT: Variable Thresholds Test for Case Control Data Analysis
• RareCover: A "Covering Algorithm" for Rare and Low Frequency Variants
• C(alpha): C-alpha Test for Protective Variants
• WSS: Weighted Sum Statistic via Rank Test
• aSum: Data-adaptive Sum Test for Protective and Deleterious Variants
• SKAT: SNP-set (Sequence) Kernel Association Test Method
• coxKM: cox Kernel Machine (http://www.hsph.harvard.edu/xlin/software.html#coxkm)

Download

• Linux binary: vartools_1.2.0_lin.tar.gz
• OS X binary: vartools_1.2.0_osx.tar.gz
• Source code: vartools_1.2.0-master.zip
• Project GitHub Repository

Documentation

Documentation help file: vartools.pdf. Please use examples for installation and quick start.

Contact

• Ilya Y. Zhbannikov, ilyaz@uidaho.edu