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Old 05-29-2012, 09:07 AM   #5
Location: Ireland

Join Date: Sep 2011
Posts: 86

Yep, the only line you need to change is UnifiedGenotyper. Add the option -glm BOTH and the output VCF file will have SNPs and indels in it. Note that if you want to do Variant Quality Score Recalibration you'll have to do some things differently if you're recalibrating indels too.
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