Changes between Version 13 and Version 14 of ImputationTool


Ignore:
Timestamp:
Sep 19, 2011 3:40:02 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationTool

    v13 v14  
    9090To impute the study vs. the reference with beagle:
    9191* mkdir study_TriTyper
    92 * Convert study ped/map data to TriTyper:
    93    * java -jar ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
     92* Convert study ped/map data to !TriTyper:
     93   * java -jar !ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
    9494* mkdir reference_TriTyper
    95 * Convert reference ped/map data to Trityper:
    96    * java -jar ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
     95* Convert reference ped/map data to !Trityper:
     96   * java -jar !ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
    9797* mkdir batches
    9898* Create batches of 300 samples of the study:
    99    * java  -jar ImputationTool.jar --mode batch --in study_TriTyper --out batches/ --size 300
     99   * java  -jar !ImputationTool.jar --mode batch --in study_TriTyper --out batches/ --size 300
    100100* mkdir reference_analyzed
    101101* Convert reference into beagle (and do some quality check as well)
    102    * java -jar ImputationTool.jar --mode ttpmh --in reference_TriTyper --hap reference_TriTyper --out reference_analyzed
     102   * java -jar !ImputationTool.jar --mode ttpmh --in reference_TriTyper --hap reference_TriTyper --out reference_analyzed
    103103* convert reference to beagle (repeat for rest chromosomes)
    104104   * java -jar linkage2beagle.jar reference_analyzed/chr1.dat reference_analyzed/chr1.ped > reference_analyzed/chr1.bgl
    105105* mkdir study_reference_compare
    106106* Perform a comparison between reference and study.
    107    * java -jar ImputationTool.jar --mode ttpmh --in study_TriTyper --hap reference_TriTyper --batch-file batches/batches.txt --out study_reference_compare
     107   * java -jar !ImputationTool.jar --mode ttpmh --in study_TriTyper --hap reference_TriTyper --batch-file batches/batches.txt --out study_reference_compare
    108108* Convert analyzed study to beagle:
    109109   * java -jar linkage2beagle.jar study_reference_compare/chr1.dat study_reference_compare/chr1.ped > reference_compare/chr1.bgl