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andersen-lab / ivar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.
https://andersen-lab.github.io/ivar/html/
GNU General Public License v3.0
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ivar variants: Output invariant sites #84

Open ksw9 opened 3 years ago

ksw9 commented 3 years ago

Hi, Thank you for your all of your work on this! I'm wondering if it is currently possible or would be possible to have an option to output invariant sites in the output VCF along with variant sites? It would be great to have depth of coverage and other annotations available for sites without an intrahost variant called, so that we could distinguish between "no-call" and reference allele genotypes, similar to options available in GATK.

Thank you in advance!

gkarthik commented 3 years ago

Hello, this is a useful feature. Thank you for suggesting it.

ksw9 commented 3 years ago

Fantastic, thank you Karthik! Is there a best way to stay updated about this? All the best, Katie

ksw9 commented 3 years ago

Dear Karthik, I hope you are doing well. I was hoping to follow-up to see if you plan to implement this? Thanks again!

gkarthik commented 3 years ago

Hey @ksw9 , sorry about the HUGE delay. I was busy with other epi projects and my thesis defense. I will try to get at this issue this month.

ksw9 commented 3 years ago

Hi Karthik, Thanks for getting back and for all of your work on iVar and genomic epi! Good luck with your defense, it will be incredible. All the best, Katie

From: Karthik @.> Date: Tuesday, June 8, 2021 at 3:49 PM To: andersen-lab/ivar @.> Cc: Katharine Walter @.>, Mention @.> Subject: Re: [andersen-lab/ivar] ivar variants: Output invariant sites (#84)

Hey @ksw9https://github.com/ksw9 , sorry about the HUGE delay. I was busy with other epi projects and my thesis defense. I will try to get at this issue this month.

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