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the difference between hard filt variant all samples together and one individual separately

hi team,
I have two close related species and there are 20 samples of each species. I used the HaplotypeCaller to call variants individually per-sample, followed by a joint genotyping step on all samples. what I'm confused is about hardfilter. Is there any difference between hard-filting variant all samples together and one individual separately. I prefer fewer variants to be filtered.


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