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What's the difference of the two parameters (-A and -a) in vg call ? #4469

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dudududu12138 opened this issue Dec 6, 2024 · 1 comment

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@dudududu12138
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dudududu12138 commented Dec 6, 2024

Hi, I used the latest version of vg. And I noticed that there are 2 parameters -A and -a. The description of them seems similar. I think every and all seems the same? But their might be some different actually. Can you explain? Thank you very much!

vg call -h 
-a, --genotype-snarls   Genotype every snarl, including reference calls (use to compare multiple samples)
-A, --all-snarls        Genotype all snarls, including nested child snarls (like deconstruct -a)
@dudududu12138
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dudududu12138 commented Dec 6, 2024

By the way, I use the gbz file and the .xg file of Minigraph Cactus graph to running vg pack and vg call, and I got 2 vcf files. I check the two vcf files are the same. And I ran with/without attaching snarl file, it doesn't seem to have an effect on the results either.

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