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How to do hard filtration with SNPs and indels together
I know that SNPS and indels can be filtered without separation by VQSR because it has a mode option allows you to specify SNPs or indels. But I didn't how to make it by hard filtration as I didn't see any mode option in VariantFiltration. I still need to use SelectVariants to separate SNPS and indels. I have read this thread http://gatkforums.broadinstitute.org/discussion/5438/should-i-run-combinevariants-on-indels-and-snps-after-vqsr-hard-filtering. But still confused. Could you please give me more information on how to do hard filtration without separating SNPs and indels.