Changes between Version 38 and Version 39 of ImputationPipeline


Ignore:
Timestamp:
Dec 6, 2011 12:33:11 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v38 v39  
    4343 * Mach / Minimach
    4444== Quality metrics ==
     45=== Convert impute2 gprobs to TPED ===
     46 * Location: http://www.bbmriwiki.nl/svn/Imputation/alex/scripts/Convert_impute2_gprobs_to_PEDMAP_beagle.ftl [[BR]]
     47This 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
    4554== Complete pipelines ==
    4655== Results ==