A question with hg19

[jbague]

Description of the bug

Hi,

I wanted to ask if it's recommended, when using the UCSC hg19 genome, to run the BaseRecalibrator step using the required files for this step from the GATK.hg19 genome (manually specifying the path), or if it’s better to skip the step with --skip_tools BaseRecalibrator. The data comes from a WES, and due to protocol limitations, it's necessary to compare somatic data using this reference genome.

Command used and terminal output

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Relevant files

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System information

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