Changes between Version 6 and Version 7 of ImputationPipeline

Timestamp:

Oct 7, 2010 2:50:06 PM (14 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -17 +17 @@
 
 '' Commands to run locally: '' 
- 1. if the dataset is in binary plink format, use plink --recode to convert back to ped+map)
- 2. convert dataset to trityper format, if it is in ped+map format.
-{{{  
-java -Xmx4g -jar ImputationTool.jar --mode pmtt --in $plinkLocation --out $trityperOutputLocation
+=== Step 1 ===
+ * According to Harm-Jan: if the dataset is in binary plink format, use plink —recode to convert back to ped+map
+ * Transform .bed   ,    .bim   and    .fam   files into ASCII format
+{{{
+/Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink --bfile /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05 --ped /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped --map CD_Finnuncorr.maf05.map --recode
+
 }}}
- 3. compare the dataset to be imputed to the reference dataset (for example HapMap2 release 24, also in TriTyper format), and remove any snps for which the haplotypes are different, or do not correlate to the reference dataset. Also remove any SNP that is not in the reference. Save the output as Ped+Map
+ * Produces the files:
 {{{
-java -Xmx4g -jar ImputationTool.jar ttpmh $trityperOutputLocation $referenceLocation $pedAndMapOutputLocation [$famFile] # supply a famfile, if you have any... it is not required
+-rw-r--r--   1 alexandroskanterakis  staff    11761120 Oct  5 12:11 plink.map
+-rw-r--r--   1 alexandroskanterakis  staff  4898208052 Oct  5 12:11 plink.ped
 }}}
+* real Execution time: 26m20.723s
+* creates rather big files 4.6G  plink.ped
+
+
+=== Step 2 ===
+
+ * Convert dataset to trityper format, if it is in ped+map format.
+{{{
+java -Xmx4g -jar /Users/alexandroskanterakis/Tools/imputation/ImputationTool/dist/ImputationTool.jar --mode pmtt --in /Users/alexandroskanterakis/Data/Finnish_cohort/ --out /Users/alexandroskanterakis/Data/Finnish_cohort/ 
+
+real    74m52.547s
+user    38m14.646s
+sys     5m25.472s
+
+}}}
+ * Files Created:
+{{{
+-rw-r--r--   1 alexandroskanterakis  staff  2449071024 Oct  5 15:05 GenotypeMatrix.dat
+-rw-r--r--   1 alexandroskanterakis  staff       46196 Oct  5 13:54 Individuals.txt
+-rw-r--r--   1 alexandroskanterakis  staff       98791 Oct  5 13:54 PhenotypeInformation.txt
+-rw-r--r--   1 alexandroskanterakis  staff    10771996 Oct  5 13:54 SNPMappings.txt
+-rw-r--r--   1 alexandroskanterakis  staff     5006368 Oct  5 13:54 SNPs.txt
+}}}
+
+=== Step 3 ===
+ * compare the dataset to be imputed to the reference dataset (for example HapMap?2 release 24, also in TriTyper? format), and remove any snps for which the haplotypes are different, or do not correlate to the reference dataset. Also remove any SNP that is not in the reference. Save the output as Ped+Map
+{{{
+java -Xmx4g -jar /Users/alexandroskanterakis/Tools/imputation/ImputationTool/dist/ImputationTool.jar --mode ttpmh --in /Users/alexandroskanterakis/Data/Finnish_cohort/ --hap /Users/alexandroskanterakis/Data/HapMap2-r24-CEU/ --out /Users/alexandroskanterakis/Data/Finnish_cohort/referenceOutput/ 
+
+real    60m53.623s
+user    30m35.172s
+sys     2m34.325s
+}}}
+
+ * Created Files (for each chromosome):
+{{{
+-rw-r--r--    1 alexandroskanterakis  staff    221184 Oct  5 16:07 chr1.dat
+-rw-r--r--    1 alexandroskanterakis  staff   1004358 Oct  5 16:06 chr1.excludedsnps.txt
+-rw-r--r--    1 alexandroskanterakis  staff    442368 Oct  5 16:07 chr1.map
+-rw-r--r--    1 alexandroskanterakis  staff    441350 Oct  5 16:07 chr1.markersBeagleFormat
+-rw-r--r--    1 alexandroskanterakis  staff   5802372 Oct  5 16:07 chr1.ped
+-rw-r--r--    1 alexandroskanterakis  staff    117708 Oct  5 16:06 chr1.warningsnps.txt
+}}}
+
+=== Steps 4-9 ===
+
  4. split the ped files in batches of 300 samples
 {{{