Changes between Version 14 and Version 15 of ImputationPipeline

Timestamp:

Nov 23, 2010 1:34:58 PM (15 years ago)

Author:

a.kanterakis

Comment:

--

ImputationPipeline

@@ -205 +205 @@
 ==== Source code ====
 http://www.bbmriwiki.nl/svn/Imputation/impute2/ConvertListsOfPedAndMapFilesToGenAndSample.py
+=== UseImpute2WithOnePhasedReferencePanel ===
+Run impute2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) with one phased reference panel.
+
+==== Parameters ====
+ * impute2Path: Path of the impute2 tool (example: /Users/alexandroskanterakis/Tools/imputation/impute_v2.1.0_MacOSX_Intel/impute2)
+ * mParameter: Fine-scale recombination map for the region to be analyzed. (example: Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt )
+ * hParameter: File of known haplotypes, with one row per SNP and one column per haplotype (example: /Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps)
+ * lParameter: Legend file(s) with information about the SNPs in the -h file(s) (example: /Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend)
+ * gParameter: File containing genotypes for a study cohort that we want to impute: (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.gen)
+ * startPos: Start position of the genomic interval to use for inference (example: 1)
+ * endPos: End position of the genomic interval to use for inference (example: 5000000)
+ * Ne: Effective size' of the population (commonly denoted as Ne in the population genetics literature) from which your dataset was sampled (example: 11418)
+ * oParameter: Name of main output file. (example: /Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.impute2)
+
+==== Example ====
+{{{
+#!div style="font-size: 80%"
+Code highlighting:
+  {{{#!python
+seImpute2WithOnePhasedReferencePanel(
+        impute2Path="/Users/alexandroskanterakis/Tools/imputation/impute_v2.1.0_MacOSX_Intel/impute2",
+        mParameter="/Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt",
+        hParameter="/Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps",
+        lParameter="/Users/alexandroskanterakis/Data/HAPMAP_1000GP/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend",
+        gParameter="/Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.gen",
+        startPos=1,
+        endPos=5000000,
+        Ne=11418,
+        oParameter="/Users/alexandroskanterakis/Data/Finnish_cohort/DividedChromosomes/Divided_1.impute2")
+  }}}
+}}}
+
+==== Source code ====
+http://www.bbmriwiki.nl/svn/Imputation/impute2/UseImpute2WithOnePhasedReferencePanel.py
 == BEABLE pipeline ==