Changes between Version 16 and Version 17 of ImputationPipeline


Ignore:
Timestamp:
Nov 23, 2010 2:17:58 PM (11 years ago)
Author:
a.kanterakis
Comment:

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  • ImputationPipeline

    v16 v17  
    240240http://www.bbmriwiki.nl/svn/Imputation/impute2/UseImpute2WithOnePhasedReferencePanel.py
    241241
    242 === UseImpute2ToImputeBedBimFamFilesWithOnePhasedReferencePanel ===
    243 Use impute2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) to impute Bed Bim Fam Files with one phased reference panel.
     242=== UseImpute2WithOnePhasedReferencePanelForCompleteChromosomeInBatches ===
     243Run impute2 (https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) with one phased reference panel. Divide the chromosome in batches.
     244
     245==== Parameters ====
     246 * impute2Path: Path of impute2 (example: /Users/alex/Tools/impute2/impute_v2.1.2_MacOSX_Intel/impute2)
     247 * mParameter: Fine-scale recombination map for the region to be analyzed (-m parameter) (example: /Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/genetic_map_chr1_combined_b36.txt)
     248 * hParameter: File of known haplotypes, with one row per SNP and one column per haplotype (-h parameter) (example: /Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.haps)
     249 * lParameter: Legend file(s) with information about the SNPs in the -h file(s) (-l parameter) (example: /Volumes/Data2/Impute/alex/hapmap3_r2_plus_1000g_jun2010_b36_ceu/hapmap3.r2.b36.allMinusPilot1CEU.chr1.snpfilt.legend)
     250 * gParameter: File containing genotypes for a study cohort that we want to impute (-g parameter) (example: /Volumes/Data2/Impute/alex/gen_sample/chr1.gen)
     251 * sizeOfBatch: Size of each batch (example: 5000000)
     252 * Ne: Effective size of the population (commonly denoted as Ne in the population genetics literature) from which your dataset was sampled (example: 11418)
     253 * oParameter: Name of main output file (-o parameter) (example: /Volumes/Data2/Impute/alex/gen_sample/)
     254 * suffix: suffix for output fil (example: chr_1_)
     255 * indexOfChromosome: Chromosome (1-22, X, Y, M) (example: 1)
    244256
    245257==== Parameters ====