Changes between Version 4 and Version 5 of ImputationTool

Timestamp:

Sep 19, 2011 2:55:33 PM (14 years ago)

Author:

a.kanterakis

Comment:

--

ImputationTool

@@ -8 +8 @@
 
 It has been written in java and managed by !NetBeans.
+
+== Documentation ==
+From the ImputationTool help screen:
+
+{{{
+ImputationTool v0.2
+
+
+------------------------
+PreProcessing
+------------------------
+
+# Create random batches of cases and controls from a TriTyper dataset. Creates a file called batches.txt in outdir.
+--mode batch --in TriTyperdir --out outdir --size batchsize
+
+------------------------
+Imputation
+------------------------
+
+# Convert Impute Imputed data into TriTyper
+--mode itt --in ImputeDir --out TriTyperDir
+------------------------
+Beagle
+------------------------
+
+# 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.
+--mode btt --in BeagleDir --tpl template --ext ext --out TriTyperDir [--fam famfile]
+
+# 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.
+--mode bttb --in BeagleDirdir --tpl template --out TriTyperDir --size numbatches
+
+------------------------
+Ped+Map (Plink files)
+------------------------
+
+# Converts Ped and Map files created by ttpmh to Beagle format
+--mode pmbg --in indir --batch-file batches.txt
+
+# 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.
+--mode ttpd --in indir --beagle beagledir --tpl template --batchdesc batchdescriptor --out outdir --fam famfile
+
+# Converts PED and MAP files to TriTyper.
+--mode pmtt --in Ped+MapDir --out TriTyperDir
+
+# Converts TriTyper file to PED and MAP files. The FAM file is optional. --split splits the ped and map files per chromosome
+--mode ttpm --in indir --out outdir [--fam famfile] [--split]
+
+# 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.
+--mode ttpmh --in TriTyperDir --hap TriTyperReferenceDir --out outdir [--fam famfile] [--batch-file batchfile] [--chr chromosome] [--exclude fileName]
+
+---------------------
+PostProcessing
+---------------------
+
+# 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.
+--mode corr --in TriTyperDir --name datasetname --in2 TriTyperDir2 --name2 datasetname2 --out outdir [--snps snplist]
+
+# 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.
+--mode corrb --in TriTyperDir --name datasetname --in2 TriTyperDir2 --name2 datasetname2 --out outdir --beagle beagleDir --tpl template --size numBatches 
+
+# Gets all the excluded snps from chrx.excludedsnps.txt with a certain call-rate threshold (0 < threshold < 1.0)
+--mode ecra --in TriTyperDir --threshold threshold
+
+# Generates R2 distribution (beagle quality score) for each batch and chromosome, and tests each batch against chromosome R2 distribution, using WilcoxonMannWhitney test
+--mode r2dist --in BeagleDir --template template --out outdir --size numbatches
+
+# Merge two TriTyper datasets
+--mode merge --in TriTyper1Dir --in2 TryTyper2Dir --out outdir
+
+}}}
+It has been written in java and managed by !NetBeans.