Changes between Version 4 and Version 5 of Test imputation pipeline


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Timestamp:
Feb 17, 2012 1:04:19 PM (12 years ago)
Author:
a.kanterakis
Comment:

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  • Test imputation pipeline

    v4 v5  
    55The reference dataset has been created from the raw VCF data of 1000 Genomes data.
    66 * Download VCF files from : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521
    7  * Export only the SNPs (filter out the indels and SVs) from VCF data by using [http://vcftools.sourceforge.net/ vcftools]
     7 * Export only the SNPs (filter out the indels and SVs) from VCF data by using [http://vcftools.sourceforge.net/ vcftools] and convert to impute2 format (hap and legend format).
    88{{{
    99vcftools \
    … …  
    1313--out ALL.chr1.phase1_release_v2.20101123.snps_indels_svs.
    1414}}}
    15 
     15    * Alternatively we coud have used the 1000 Genomes reference panel in impute2 format (legend and hap files) from the impute2 website: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download_reference_data
    1616The study panel is an artificial genotype dataset. Created by
    1717The study panel is an artificial genotype dataset. Created by