For whatever reason genesis output files are kind of stupid and we need to account for a couple more cases than with RVTests.
1). Genesis does not include the REF/ALT allele in the output so we need to first merge the genesis output file with the info file by chr/pos to add additional information (REF/ALT). Once we have these, we need to create the variant ID like we do normally and everything can proceed like with RVTests output
2) Genesis sumstats output files apparently do not always have the Est. (beta value) columns. My genesis output from the handedness study (binary trait) only have the Score columns (z-score). Need to account for this corner case when beta-value columns are missing. Also should perhaps let the user choose whether they want to use z-score or betas. Perhaps default to beta's and only get z-scores for binary traits?
For whatever reason genesis output files are kind of stupid and we need to account for a couple more cases than with RVTests.
1). Genesis does not include the REF/ALT allele in the output so we need to first merge the genesis output file with the info file by chr/pos to add additional information (REF/ALT). Once we have these, we need to create the variant ID like we do normally and everything can proceed like with RVTests output
2) Genesis sumstats output files apparently do not always have the Est. (beta value) columns. My genesis output from the handedness study (binary trait) only have the Score columns (z-score). Need to account for this corner case when beta-value columns are missing. Also should perhaps let the user choose whether they want to use z-score or betas. Perhaps default to beta's and only get z-scores for binary traits?