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Mutation calling rules for targeted sequencing of 4 genes

Dear GATK team,
we are validating our findings on a large cohort of 150 patient samples. We are sequencing only 4 genes using Fluidigm amplicons on MiSeq system. Since there are only 4 genes and some of the GATK pipeline steps (i.e recalibration etc. ) may not be appropriate ( I assumed this), what steps do you suggest to utilize to call for variants.
Also, what rules do you suggest, such as filtering based on QUAL, QD and read depth. Is there any suggestion.

Also what read depth would you recommend to select a variant as significant.

I appreciate your help and time.
Thanks
Adrian

Answers

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