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Old 09-29-2011, 07:56 AM   #1
cbeck
Junior Member
 
Location: Montreal

Join Date: Sep 2011
Posts: 6
Default 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

?
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