Changes between Version 17 and Version 18 of DataConcordance


Ignore:
Timestamp:
May 3, 2011 11:38:52 AM (14 years ago)
Author:
laurent
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • DataConcordance

    v17 v18  
    1414 * See [[GoNL_Immunochip_Data_Preparation]] about how the Immunochip data was processed
    1515 * See [https://www.broad.harvard.edu/gsa/wiki/index.php/LiftOverVCF.pl GATK LiftOverVCF] about how to liftover a VCF file from one reference to another
    16 
     16   * IMPORTANT: Check your VCF file header as some versions of the GATK  liftover tool (e.g. v1.0.5083) might mix the individuals in the header  (sort alphabetically rather than preserve original order). If the order is changed, then you should copy/paste the original order from the source VCF file.
    1717=== Concordance calculation using [http://vcftools.sourceforge.net/ VCFTools] ===
    1818To calculate the concordance between the different files, [http://vcftools.sourceforge.net/ VCFTools] was used. More specifically: <pre>vcftools --vcf /data/lfrancioli/immunochip/hg19/GvNL.hg19.final.vcf --indv ${sample} --diff /data/lfrancioli/results/pilot/${sample}.human_g1k_v37.immuno.vcf --diff-site-discordance --diff-indv-discordance --diff-discordance-matrix</pre> This computes the concordance per file, site and individual as well as a discordance matrix. This was applied on a sample level so only the file, site and discordance matrix where actually used.