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VariantFiltration and VariantRecalibrator
I have 2 questions:
I want to use the VariantFiltration after HaplotypeCaller. There are different filtering recommendations for SNPs and INDELs. How should I run the VariantFiltration? Should I create a separated vcf for SNPs and INDELs or is there a mode to use?
The second question is regarding VariantRecalibrator. It is recommended to run it with several samples. What does it mean - these samples should be family related or should they be from the same sequencing run? Since, currently I run each sample separately, but I do have many samples to analyze. All were sequenced at the same sequencing platform, by the same lab, but not necessarily at the same sequencing run. Can I use all together for the VariantRecalibrator?
Many thanks for your help,