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Annotation using dbSNP common variants (MAF >0.01)
A question on known indel files to use with RealignerTargetCreator, in case if we're looking for novel mutations based on dbSNP common variants (MAF >0.01). I noticed that when I used the recommended indel files (both 1000genomes phase 1 and Mills gold standard) for IndelRealignment and then further I used dbSNP common variants for VariantAnnotation on VCF, it reported many novel variants, mostly of them were indels. So I'm suspecting that it could be probably due the known Indel files given to Realignment, as it ignore ALL the known indels sites from realignment, which might get reported later in the novel list.
Hope you got the issue.
What do you suggest here - ReAlignment without any known indel file(s) or just with the common variants file?