Changes between Version 18 and Version 19 of DataConcordance


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Timestamp:
Jun 16, 2011 7:09:18 AM (6 years ago)
Author:
mswertz
Comment:

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  • DataConcordance

    v18 v19  
    1616   * 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] ===
    18 To 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.
     18To calculate the concordance between the different files, [http://vcftools.sourceforge.net/ VCFTools] was used. More specifically:
     19
     20{{{
     21vcftools --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
     22
     23}}}
     24 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.
    1925
    2026=== Concordance aggregation using home-made scripts ===