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sridnona / cb_sniffer

mutation(barcode) caller for 10x single cell data
GNU General Public License v3.0
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How to input indel variant file? #8

Open lightfromdark opened 4 years ago

lightfromdark commented 4 years ago

Hello, For SNV, the software works good. However, I do not know how to input Indel variant file? could you give a template for that. Especially, I am not sure which start location should use and how long I should include the indel sequence? thanks a lot for help, Will

sridnona commented 4 years ago

Indels calling has some issues currently and i would not advise using it for the same.

Sid

lightfromdark commented 4 years ago

Thanks a lot for your reply.

On Thu, Mar 26, 2020, 12:05 AM sridnona notifications@github.com wrote:

Indels calling has some issues currently and i would not advise using it for the same.

Sid

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sridnona commented 4 years ago

@lightfromdark recently merged indel support, please give it a try.

Thanks Sid

lightfromdark commented 4 years ago

Sid,

Great, thanks a lot for your continuous support.

If I have further question, will let you know,

Best wishes,

Weiguo

From: sridnona [mailto:notifications@github.com] Sent: Friday, June 12, 2020 2:00 PM To: sridnona/cb_sniffer cb_sniffer@noreply.github.com Cc: lightfromdark wgfeng2009@gmail.com; Mention mention@noreply.github.com Subject: Re: [sridnona/cb_sniffer] How to input indel variant file? (#8)

@lightfromdark https://github.com/lightfromdark recently merged indel support, please give it a try.

Thanks Sid

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dcruz5h commented 2 years ago

I have a similar problem. I have two samples, one with a TT--TG deletion (reference: TTTGTG) and one with a TG--GC (reference TGGAGT). it seems that cb_sniffer does not accept deletions. Or is there a specific format for deletions for the variant file ?

sridnona commented 2 years ago

Can you share the deletion in this format

chr     st      stop    reference