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Combine consensus and variants #34

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tseemann opened this issue Apr 9, 2020 · 2 comments
Open

Combine consensus and variants #34

tseemann opened this issue Apr 9, 2020 · 2 comments
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@gkarthik

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@tseemann
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tseemann commented Apr 9, 2020

It is inefficient to run both of these, when they do nearly the same thing, and both use the same mpileup.

Can you merge them?
@IsabelFE
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IsabelFE commented Jun 7, 2021

I agree, it would be more efficient in one step

@gkarthik gkarthik self-assigned this Jun 8, 2021
@mikeyweigand
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Chiming in here to say it would be helpful if consensus would report a list of changes applied based on the given parameters, which is kinda saying the same thing, so long as the variants report also includes sites changed to "N" due to low coverage.

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@gkarthik gkarthik

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@tseemann @gkarthik @IsabelFE @mikeyweigand