Changes between Version 12 and Version 13 of ImputationTool


Ignore:
Timestamp:
Sep 19, 2011 3:39:15 PM (14 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationTool

    v12 v13  
    7979}}}
    8080
     81=== Example ===
     82This is a common scenario using !ImputationTool: Suppose that we have the following directory structure:
     83* study
     84   * study.ped
     85   * study.map
     86* reference
     87   * reference.ped
     88   * reference.map
     89
     90To impute the study vs. the reference with beagle:
     91* mkdir study_TriTyper
     92* Convert study ped/map data to TriTyper:
     93   * java -jar ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
     94* mkdir reference_TriTyper
     95* Convert reference ped/map data to Trityper:
     96   * java -jar ImputationTool.jar --mode pmtt --in study/ --out study_TriTyper
     97* mkdir batches
     98* Create batches of 300 samples of the study:
     99   * java  -jar ImputationTool.jar --mode batch --in study_TriTyper --out batches/ --size 300
     100* mkdir reference_analyzed
     101* 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
     103* convert reference to beagle (repeat for rest chromosomes)
     104   * java -jar linkage2beagle.jar reference_analyzed/chr1.dat reference_analyzed/chr1.ped > reference_analyzed/chr1.bgl
     105* mkdir study_reference_compare
     106* 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
     108* Convert analyzed study to beagle:
     109   * java -jar linkage2beagle.jar study_reference_compare/chr1.dat study_reference_compare/chr1.ped > reference_compare/chr1.bgl
     110* mkdir RESULTS
     111* And now time for the imputation step (beagle needed)
     112   * java -jar beagle.jar phased=reference_analyzed/chr1.bgl unphased=study_reference_compare/chr1.bgl markers=reference_analyzed/chr1.markersBeagleFormat missing=0 out=RESULTS/output
    81113=== The !TriTyper Format ===
    82114!TriTyper is a binary format to store genotype information, including insertion, deletion and expression data,  providing very efficient read/write/seek methods.