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Clarification of parameters for HaplotypeCaller
Hi I'm new to GATK and am looking into using HaplotypeCaller to call chloroplast variants in a plant. I am interested in both the variant sites and invariant sites in my sample (relative to my reference).
I know that in order to get confidence in homozygous reference sites, I should use:
But how does this differ from
Also can someone please clarify the difference between
PS I am also looking into Mutect2 for calling chloroplast variation but am not quite convinced that a somatic caller is what I want here so for now would just like to understand HaplotypeCaller better. Thanks!