Test-drive the GATK tools and Best Practices pipelines on Terra
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confusion Base quality score recalibration
i need to know about --solid_recal_mode : SET_Q_ZERO
\ --solid_nocall_strategy : LEAVE_READ_UNRECALIBRATED
i have problem in understanding these parameter though i read this explanation
--solid_recal_mode : SET_Q_ZERO
Set reference inserted bases and the previous base (because of color space alignment details) to Q0. This is the default option
When a no call is detected throw an exception to alert the user that recalibrating this SOLiD data is unsafe. This is the default option.
can you explain in simple way