How to input indel variant file?

[lightfromdark]

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]

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

Sid

[lightfromdark]

Thanks a lot for your reply.

…

On Thu, Mar 26, 2020, 12:05 AM sridnona ***@***.***> wrote: Indels calling has some issues currently and i would not advise using it for the same. Sid — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB75SBPEMP3RKDFRREXXPVTRJLPBTANCNFSM4LMVZP5Q> .

[sridnona]

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

Thanks
Sid

[lightfromdark]

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 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#8 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB75SBPDNZPY2YRWQAI4QU3RWJ3L3ANCNFSM4LMVZP5Q> . <https://github.com/notifications/beacon/AB75SBLR4AY3V7SPTZERO73RWJ3L3A5CNFSM4LMVZP52YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEZNAZFI.gif>

[dcruz5h]

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]

Can you share the deletion in this format

chr     st      stop    reference