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GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Reference calls by HaplotypeCaller

Hi there,

I'm trying to run the HaplotypeCaller in GATK2.5. I hope to get the confident reference calls as UnifiedGenotyper outputs, so I set the option "-out_mode EMIT_ALL_CONFIDENT_SITES". However, I notice the total number of reference calls HaplotypeCaller makes is really small. I'm wondering could you provide any information on how HaplotyperCaller decides where to/not to output the reference calls please?

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  • jianljianl Member

    To be more specific, I'm working with single sample. I'm wondering is there any other option that I didn't correctly set or do I have to feed in multiple samples to get the ref call at positions where at least one sample showing variant?

    Any help would be appreciated!

    Thanks,
    Jian

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