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  • cbeck
    Junior Member
    • Sep 2011
    • 6
    #1

    Merging samples to get cross-experiment variation

    So we have several flow cells worth of indexed samples generated from targeted resequencing and I want to merge all of the variant calls for all samples with the ability to distinguish between no-call and reference-call for all samples. Would I be best advised to

    a) merge all the bam files and generate the vcf from there
    or
    b) take all the individual sample vcfs and merge them with vcftools

    ?
    Tags: None
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