| | 45 | === Convert impute2 gprobs to TPED === |
| | 46 | * Location: http://www.bbmriwiki.nl/svn/Imputation/alex/scripts/Convert_impute2_gprobs_to_PEDMAP_beagle.ftl [[BR]] |
| | 47 | This method is suitable to convert results from impute2 imputation to TPED. You can define an R2 threshold. The R2 is the allelic R2 according to http://www.sciencedirect.com/science/article/pii/S0002929709000123#sec2.7.2 . You can copy the TFAM from the original study in order to have a complete TPED / TFAM dataset. [[BR]] |
| | 48 | Options: |
| | 49 | * input_impute2_gprobs_filename : The gprobs file generated from impute2 |
| | 50 | * output_TPED_filename : The output TPED filename |
| | 51 | * output_stats_filename : The file where the R2 estimation will be printed. It will contain ALL the R2 values not only these surpassing the threshold |
| | 52 | * chromosome : The chromosome of this study |
| | 53 | * r2_threshold : The R2 threshold |
