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I am adapting a two-year old pipeline, which includes UnifiedGenotyper to call variants. I would like to update this to the HaplotypeCaller.
In the command for the UnifiedGenotyper there is an option --metrics_file. I cannot find reference to this in the GATK documentation - do you know what it is and whether I can use it with HaplotypeCaller as well?
Also, do I understand correctly that using HaplotypeCaller to call variants means you don't have to carry out the local realignment around indels step prior to this?
Thanks very much,