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Varian quality recalibration annotations.

lalirlalir CanadaMember

Hello,
What annotations are recommended to be used for the variant recalibrator for an exome sequencing project? I am using the Ion proton system so my VCF files are automatically generated after the sequencing run. Also, would I still have to mark duplicates and realign indels in my BAM files before viewing them on a genome viewer like IGV? Since I already have my VCF files, I don't know if this will be necessary.
Thank you, these forums are very helpful!
Ricky

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