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Base Recalibration -Second recalibration table

Hello

I need some advice in the base recalibration step. I have build the recalibration model and have got the recalibrated bam file. To create the after model to estimate the remaining error, should I give the recalibrated bam file as input or the original bam file as input?. I am in the step to create the second recalibration table. But, not sure if the model estimates the remaining error using the recalibrated bam file.

Thanks

base gatk ngs recalibration
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updated by alexcouzens • alexcouzens • written by priya.bmg • priya.bmg

I was wondering if creating the second recalibration table ('after model') was still possible.

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written by alexcouzens • alexcouzens

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