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Clarification of parameters for HaplotypeCaller

julleejullee Member
edited October 2018 in Ask the GATK team

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:

--emit-ref-confidence BP_RESOLUTION 

But how does this differ from



Also can someone please clarify the difference between




Many thanks!

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!


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @jullee

    --output-mode EMIT_ALL_CONFIDENT_SITES
    This specifies which type of calls should be in the output.
    --emit-ref-confidence BP_RESOLUTION
    This specifies reference confidence scores and not which sites should be in the output, like the previous option. For more information follow this link.
    Bases with a quality below this threshold will be reduced to the minimum usable quality score (6), but they will still be called.
    Bases with a quality below this threshold will not be used for calling.

    I hope this helps. For more information please refer to the tool doc for HaplotypeCaller.


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