Changes between Version 13 and Version 14 of ImputationTool

Timestamp:

Sep 19, 2011 3:40:02 PM (13 years ago)

Author:

a.kanterakis

Comment:

--

ImputationTool

@@ -90 +90 @@
 To impute the study vs. the reference with beagle:
 * mkdir study_TriTyper
-* Convert study ped/map data to TriTyper: 
-   * java -jar ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
+* Convert study ped/map data to !TriTyper: 
+   * java -jar !ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
 * mkdir reference_TriTyper
-* Convert reference ped/map data to Trityper: 
-   * java -jar ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
+* Convert reference ped/map data to !Trityper: 
+   * java -jar !ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
 * mkdir batches
 * Create batches of 300 samples of the study: 
-   * java  -jar ImputationTool.jar --mode batch --in study_TriTyper --out batches/ --size 300
+   * java  -jar !ImputationTool.jar --mode batch --in study_TriTyper --out batches/ --size 300
 * mkdir reference_analyzed
 * Convert reference into beagle (and do some quality check as well)
-   * java -jar ImputationTool.jar --mode ttpmh --in reference_TriTyper --hap reference_TriTyper --out reference_analyzed
+   * java -jar !ImputationTool.jar --mode ttpmh --in reference_TriTyper --hap reference_TriTyper --out reference_analyzed
 * convert reference to beagle (repeat for rest chromosomes)
    * java -jar linkage2beagle.jar reference_analyzed/chr1.dat reference_analyzed/chr1.ped > reference_analyzed/chr1.bgl
 * mkdir study_reference_compare
 * Perform a comparison between reference and study.
-   * java -jar ImputationTool.jar --mode ttpmh --in study_TriTyper --hap reference_TriTyper --batch-file batches/batches.txt --out study_reference_compare
+   * java -jar !ImputationTool.jar --mode ttpmh --in study_TriTyper --hap reference_TriTyper --batch-file batches/batches.txt --out study_reference_compare
 * Convert analyzed study to beagle:
    * java -jar linkage2beagle.jar study_reference_compare/chr1.dat study_reference_compare/chr1.ped > reference_compare/chr1.bgl