Changes between Version 4 and Version 5 of ImputationTool


Ignore:
Timestamp:
Sep 19, 2011 2:55:33 PM (13 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationTool

    v4 v5  
    88
    99It has been written in java and managed by !NetBeans.
     10
     11== Documentation ==
     12From the ImputationTool help screen:
     13
     14{{{
     15ImputationTool v0.2
     16
     17
     18------------------------
     19PreProcessing
     20------------------------
     21
     22# Create random batches of cases and controls from a TriTyper dataset. Creates a file called batches.txt in outdir.
     23--mode batch --in TriTyperdir --out outdir --size batchsize
     24
     25------------------------
     26Imputation
     27------------------------
     28
     29# Convert Impute Imputed data into TriTyper
     30--mode itt --in ImputeDir --out TriTyperDir
     31------------------------
     32Beagle
     33------------------------
     34
     35# Convert beagle files (one file/chromosome) to TriTyper. Filetemplate is a template for the batch filenames, The text CHROMOSOME will be replaced by the chromosome number.
     36--mode btt --in BeagleDir --tpl template --ext ext --out TriTyperDir [--fam famfile]
     37
     38# Convert batches of beagle files (multiple files / chromosome) to trityper files. Filetemplate is a template for the batch filenames, The text CHROMOSOME will be replaced by the chromosome number, BATCH by the batchname.
     39--mode bttb --in BeagleDirdir --tpl template --out TriTyperDir --size numbatches
     40
     41------------------------
     42Ped+Map (Plink files)
     43------------------------
     44
     45# Converts Ped and Map files created by ttpmh to Beagle format
     46--mode pmbg --in indir --batch-file batches.txt
     47
     48# Converts TriTyper file to Plink Dosage format. Filetemplate is a template for the batch filenames, The text CHROMOSOME will be replaced by the chromosome number, BATCH by the batchname.
     49--mode ttpd --in indir --beagle beagledir --tpl template --batchdesc batchdescriptor --out outdir --fam famfile
     50
     51# Converts PED and MAP files to TriTyper.
     52--mode pmtt --in Ped+MapDir --out TriTyperDir
     53
     54# Converts TriTyper file to PED and MAP files. The FAM file is optional. --split splits the ped and map files per chromosome
     55--mode ttpm --in indir --out outdir [--fam famfile] [--split]
     56
     57# Converts TriTyper dataset to Ped+Map concordant to reference (hap) dataset. Supply a batchfile if you want to export in batches. Supply a chromosome if you want to export a certain chromosome.
     58--mode ttpmh --in TriTyperDir --hap TriTyperReferenceDir --out outdir [--fam famfile] [--batch-file batchfile] [--chr chromosome] [--exclude fileName]
     59
     60---------------------
     61PostProcessing
     62---------------------
     63
     64# Correlates genotypes of imputed vs non-imputed datasets. Saves a file called correlationOutput.txt in outdir, containing correlation per chromosome as well as correlation distribution.
     65--mode corr --in TriTyperDir --name datasetname --in2 TriTyperDir2 --name2 datasetname2 --out outdir [--snps snplist]
     66
     67# Correlates genotypes of imputed vs non-imputed datasets. Also take Beagle imputation score (R2) into account. Saves a file called correlationOutput.txt in outdir, containing correlation per chromosome as well as correlation distribution.
     68--mode corrb --in TriTyperDir --name datasetname --in2 TriTyperDir2 --name2 datasetname2 --out outdir --beagle beagleDir --tpl template --size numBatches
     69
     70# Gets all the excluded snps from chrx.excludedsnps.txt with a certain call-rate threshold (0 < threshold < 1.0)
     71--mode ecra --in TriTyperDir --threshold threshold
     72
     73# Generates R2 distribution (beagle quality score) for each batch and chromosome, and tests each batch against chromosome R2 distribution, using WilcoxonMannWhitney test
     74--mode r2dist --in BeagleDir --template template --out outdir --size numbatches
     75
     76# Merge two TriTyper datasets
     77--mode merge --in TriTyper1Dir --in2 TryTyper2Dir --out outdir
     78
     79}}}
     80It has been written in java and managed by !NetBeans.