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GATK (version 3.4-0.d9)

Using reference genome:

-R,‑‑reference_sequence <reference_sequence>

Select interval subset to operate on?:

Select covariates for on-the-fly recalibration?:

Set computational options (cpu, mem)?:

Analysis Type:

Input all BAM files in a single command:

Input file containing sequence data (BAM):

-I, ‑‑input_file

Configure Optional Parameters: