UGENE Forum - SNP caller

Jul 9^th, 2012 at 4:57pm

kenkl Offline
Junior Member

Posts: 73

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

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Reply #1 - Jul 10^th, 2012 at 12:06pm

Yuriy Vaskin Offline
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Posts: 138

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!

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Reply #2 - Jul 10^th, 2012 at 12:11pm

Yuriy Vaskin Offline
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Oh, it's in Java Sad

I don't think we can embed it in that case.

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

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Reply #3 - Jul 27^th, 2012 at 1:01pm

kenkl Offline
Junior Member

Posts: 73

Hi there!

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

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Reply #4 - Jul 27^th, 2012 at 1:07pm

Yuriy Vaskin Offline
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Unoptimized version will be available soon...

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Reply #5 - Jul 30^th, 2012 at 8:14am

kenkl Offline
Junior Member

Posts: 73

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

Thanks!

Regards,
Ken

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Reply #6 - Jul 31^st, 2012 at 6:44pm

Yuriy Vaskin Offline
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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.

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Reply #7 - Aug 1^st, 2012 at 8:03am

kenkl Offline
Junior Member

Posts: 73

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

Regards,
Ken

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Reply #8 - Aug 1^st, 2012 at 8:15am

kenkl Offline
Junior Member

Posts: 73

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

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Reply #9 - Aug 1^st, 2012 at 1:17pm

Yuriy Vaskin Offline
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Posts: 138

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

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