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Old 01-18-2012, 04:49 AM   #59
ulz_peter
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Location: Graz, Austria

Join Date: Feb 2010
Posts: 219
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Hi Mali Salmon,

I imported the document to the Seq-Wiki (see http://seqanswers.com/wiki/How-to/exome_analysis). The problem is: Variant recalibration doesn't really work for single-exome analyses. In the updated version (which is already kind of out-of-date) in the Seq Wiki, I already wrote that I got back to SNP filtering using VariantFiltration as I often got a lot of error messages trying to do Variant recalibration on a single sample.

There is a link to the GATK Homepage on the wiki. If you still want to do Variant Quality Score Recalibration I'd recommend you stick to their guidelines.

Hope that helps (and I am really happy some people really read the guideline)
Best regards,
Peter
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