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https://forum.ugene.net/forum/YaBB.pl General Category >> Feature Requests >> SNP caller https://forum.ugene.net/forum/YaBB.pl?num=1341827832 Message started by kenkl on Jul 9^th, 2012 at 4:57pm

Title: SNP caller
Post by kenkl on Jul 9^th, 2012 at 4:57pm

Hi there,

I think it would be really useful if ugene can add SNP caller into its workflow designer. E.g. of such tools is SNPdigger

Regards,
Ken

Title: Re: SNP caller
Post by Yuriy Vaskin on Jul 10^th, 2012 at 12:06pm

Hi Kenneth,

Actually, we are working on implementation of an SNP caller in WD. It's based on samtools mpileup.

First version will be available soon.

Thanks for advising SNPdigger. I've checked it out. It works with CAP3 output which is integrated into UGENE.

We'll consider integration of SNPdigger later (https://ugene.unipro.ru/tracker/browse/UGENE-1085).

Thank you!

Title: Re: SNP caller
Post by Yuriy Vaskin on Jul 10^th, 2012 at 12:11pm

Oh, it's in Java :(
I don't think we can embed it in that case.

You could try to run it as an external tool in WD.

Title: Re: SNP caller
Post by kenkl on Jul 27^th, 2012 at 1:01pm

Hi there!

Glad to hear that SNP caller will be incorporated. When will it be implemented yea?

Title: Re: SNP caller
Post by Yuriy Vaskin on Jul 27^th, 2012 at 1:07pm

Unoptimized version will be available soon...

Title: Re: SNP caller
Post by kenkl on Jul 30^th, 2012 at 8:14am

Alright, thanks! Besides, just want to know is Cap3 and Aln format interchangeable in UGENE?

Thanks!

Regards,
Ken

Title: Re: SNP caller
Post by Yuriy Vaskin on Jul 31^st, 2012 at 6:44pm

Hi!

A simple SNP caller has been implemented.
It compares consnsus and reference in Assembly Browser.
It's available here: http://ugene.unipro.ru/snapshot.html

Open an assembly, load a reference sequence. Right click on consensus and click "Export Consensus Variations..."

What do you mean by "interchangeable ". Cap3 outputs data in ACE format it's an alignment format. You can open it and export in any alignment format supported by UGENE.

Title: Re: SNP caller
Post by kenkl on Aug 1^st, 2012 at 8:03am

Thanks! Will try it out and give feedback to you!

Regards,
Ken

Title: Re: SNP caller
Post by kenkl on Aug 1^st, 2012 at 8:15am

Hi there,

Can the snp caller do something like this one:
http://sourceforge.net/projects/msa2snp/

It highlights the SNPs or variations.

Thanks!

Regards,
Ken

Title: Re: SNP caller
Post by Yuriy Vaskin on Aug 1^st, 2012 at 1:17pm

There is no SNP highlighting in Multiple Alignment Editor, but the function is availabele in Assembly Browser.