Changes between Version 10 and Version 11 of Impute2Pipeline


Ignore:
Timestamp:
Apr 25, 2013 8:06:38 PM (8 years ago)
Author:
Morris Swertz
Comment:

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  • Impute2Pipeline

    v10 v11  
    77* Pre-processing of study data
    88 1. Liftover PED/MAP files from build 36 to build 37
    9  1. Quality control of study data
     9 2. Quality control of study data
    1010* Analysis
    11  1. Phasing the study data
    12  1. Imputing the study data
    13 A list of used software and versions can be found on the bottom of this page.
     11 3. Phasing the study data
     12 4. Imputing the study data
     13Detailed description and a list of used software and versions can be found on the bottom of this page.
    1414
    1515All analysis jobs are generated using [http://www.molgenis.org/wiki/ComputeStart MOLGENIS Compute], more information about MOLGENIS Compute and the other analysis pipelines can be found here: https://github.com/molgenis/molgenis-pipelines
     
    1717== Paper ready summary ==
    1818
    19 TODO.
     19You can use the following text in your paper:
     20
     21TODO. Including citations.
    2022
    2123== Reference data ==
     
    2325 * GoNL release 4, 499 unrelated individuals, 998 haplotypes
    2426
    25 == Pre processing of study data ==
    26  === Liftover PED/MAP files from build 36 to build 37 ===
     27== Detailed description ==
     28=== Step 1: Liftover PED/MAP files from build 36 to build 37 ===
    2729 * Location: https://github.com/molgenis/molgenis-pipelines/blob/master/compute4/Liftover_genome_build_PEDMAP/protocols/liftoverPEDMAP.ftl
    2830 [[br]]This protocol applies the following steps:
     
    3335 * Create new plink data without unmapped SNPs using [http://pngu.mgh.harvard.edu/~purcell/plink/ Plink].
    3436 [[br]]
    35  === Quality control of study data ===
     37 === Step 2: Quality control of study data ===
    3638 * Location: https://github.com/molgenis/molgenis-pipelines/blob/master/compute4/Imputation_imputationtool_studyQC/protocols/studyQC.ftl
    3739 [[br]]This protocol applies QC to the study data using [http://genenetwork.nl/wordpress/imputationtool/ imputationTool]. This tool employs a binary format, called [http://genenetwork.nl/wordpress/trityper/ TriTyper] for rapid loading of big genotypic data. ImputationTool performs the following checks:
     
    4345 [[br]]
    4446 [[br]]
    45 == Analysis ==
    46  === Phasing the study data ===
     47 === Step 3: Phasing the study data ===
    4748 * Location: https://github.com/molgenis/molgenis-pipelines/blob/master/compute4/Imputation_shapeit_phasing/protocols/shapeitPhasing.ftl
    4849 [[br]]This protocol phases the study data using [http://shapeit.fr/ shapeit], study data can be in the following formats: Ped/Map, Bed/Bim, Gen/Haps.
     
    5152 * Phase the study data using the map files.
    5253 [[br]]
    53  === Imputing study data ===
     54 === Step 4: Imputing study data ===
    5455 * Location: https://github.com/molgenis/molgenis-pipelines/blob/master/compute4/Imputation_impute2/protocols/impute2Imputation.ftl
    5556 [[br]]This protocol imputes the study data in chromosome bins of 5million bases using [http://mathgen.stats.ox.ac.uk/impute/impute_v2.html Impute2]. Afterwards the results per chromosome bin are merged into full chromosomes.