The adjusted Wu test is described by Ueki and Cordell (2012) and is a corrected version of a test proposed by Wu et al. (2010) . The test is based on the 4 estimated haplotype frequencies between the two SNPs that are being tested (calculated using the EM algorithm in CASSI).

## 5.1 Options

The options that are specific to the adjusted Wu test are:

Option Description
-awu perform the adjusted Wu test
-awu-thcc t p-value threshold for case/control test
-awu-thco t p-value threshold for case only test
-awu-th t p-value threshold for either test
-awu-cc-only perform the case/control test only
-awu-co-only perform the case only test only
-awu-so suppress results of test

CASSI performs both the case only test and case/control test for each pair of tested SNPs by default. SNPs that are too close for the case only test, as definded by the -gap option, are not tested. The results of the test are recorded for the pair of SNPs if either p-value threshold is met. Both thresholds may be set simultaneously by using the -awu-th option. The default value for both thresholds is 0.0001.

For other basic options see section 3.2.

## 5.2 Output File

The output file from running an adjusted Wu SNP interaction analysis using CASSI will look something like the following:

SNP1 CHR1 ID1 BP1 SNP2 CHR2 ID2 BP2 AWU_CASE_LOG_OR AWU_CASE_SE AWU_CTRL_LOG_OR AWU_CTRL_LOG_SE AWU_CC_CHISQ AWU_CC_P AWU_CO_CHISQ AWU_CO_P
1306 1 rs285785 6939568 542 1 rs2657173 4519034 0.663321 0.154558 0.247584 0.158968 3.51587 0.0607836 18.4189 1.77292e-05
1306 1 rs285785 6939568 544 1 rs26414414 4519523 0.671198 0.154619 0.208327 0.15861 4.36672 0.0366475 18.844 1.41854e-05
1349 1 rs150628 7172817 572 1 rs22312963 4581596 -0.734064 0.180251 -0.00671448 0.178903 8.20253 0.0041832 16.5849 4.65207e-05
1352 1 rs185794 7190018 639 1 rs794332 4807931 -0.604667 0.13482 -0.299917 0.133023 2.58902 0.107607 20.1152 7.29157e-06
...


The first line is a header labelling the columns of the results file. The SNP details for the pair of SNPs are given firstly followed by values calculated from the joint effects tests. Results are given for both the case only test and for the case/control test regardless of which p-value was significant enough to record the pair of SNPs. The case only test assumes that the two SNPs are in linkage equilibrium in the general population, so care must be taken in interpreting results with SNPs that are near one another. See Ueki and Cordell (2012).

AWU_CASE_LOG_OR is the log odds ratio for association in the cases.

AWU_CASE_SE is the standard error of AWU_CASE_LOG_OR.

AWU_CTRL_LOG_OR is the log odds ratio for association in the controls.

AWU_CTRL_SE is the standard error of AWU_CTRL_LOG_OR.

AWU_CC_CHISQ is the $\inline \chi^2 \small$ test statistic with one degree of freedom for the case/control test.

AWU_CC_P is the corresponding p-value for the case/control test.

AWU_CO_CHISQ is the $\inline \chi^2 \small$ test statistic with one degree of freedom for the case only test.

AWU_CO_P is the corresponding p-value for the case only test.