Changes between Version 17 and Version 18 of ImputationPipeline

Timestamp:

Nov 23, 2010 2:21:45 PM (13 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -255 +255 @@
  * indexOfChromosome: Chromosome (1-22, X, Y, M) (example: 1)
 
-==== Parameters ====
- * plink_path: Path to plink executable (example: /Users/alexandroskanterakis/Tools/plink/plink-1.07-mac-intel/plink)
- * bbf_path: Path to BED, BIM, FAM file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05)
- * ped_path: Filename of exported PED file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.ped)
- * map_path: Filename of exported MAP file (example: /Users/alexandroskanterakis/Data/Finnish_cohort/CD_Finnuncorr.maf05.map)
- * output_divided_path: Directory where the divided according to chromosomes Pem and Map files will be exported (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes)
- * suffix: Suffix of the exported files (example: output_)
- * gtoolPath: Path of gtool (example: /Users/alexandroskanterakis/Tools/gtool/gtool)
- * impute2Path: Path of impute2: (example: /Users/alexandroskanterakis/Tools/imputation/impute_v2.1.0_MacOSX_Intel/impute2)
- * mParameter: Fine-scale recombination map for the region to be analyzed
- * hParameter: File of known haplotypes, with one row per SNP and one column per haplotype
- * lParameter: Legend file(s) with information about the SNPs in the -h file(s)
-
+==== Example ====
+{{{
+#!div style="font-size: 80%"
+Code highlighting:
+  {{{#!python
+UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches(
+        impute2Path = "/Users/alex/Tools/impute2/impute_v2.1.2_MacOSX_Intel/impute2" ,
+        mParameter = "/Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt" ,
+        hParameter = "/Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps" ,
+        lParameter = "/Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend" ,
+        gParameter = "/Volumes/Data2/Impute/alex/gen_sample/chr1.gen" ,
+        sizeOfBatch = 5000000 ,
+        Ne = 11418 ,
+        oParameter = "/Volumes/Data2/Impute/alex/gen_sample/" ,
+        suffix = "chr_1_" ,
+        indexOfChromosome = "1")
+  }}}
+}}}
+
+==== Source Code ====
+http://www.bbmriwiki.nl/svn/Imputation/impute2/UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches.py
 == BEABLE pipeline ==