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Old 04-27-2012, 05:58 AM   #2
Location: Ireland

Join Date: Sep 2011
Posts: 86

The Mills and 1000G gold standard indels are a very stringently curated list of indels. For the purposes of indel realignment in GATK you probably want one or more of the broader sets from the GATK bundle instead, though which ones I'm not completely sure.

Overall though, your workflow looks fine. Bear in mind though, that it will only call SNPs and not indels (but since you're calling your output file resultSNPs I assume you know that already).
Rocketknight is offline   Reply With Quote