SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Annotate total variants against reference genome using CLC genomics? Karlos Illumina/Solexa 0 02-26-2015 07:13 AM
annotate ID after using DESeq willemate Bioinformatics 6 04-02-2014 07:31 PM
CASIM: Variants Picking the best software casim UK - Cambridge 0 04-18-2013 12:30 PM
Annotate coordinates giuliano stirparo Bioinformatics 1 01-10-2013 10:55 PM
Annotate memyselfandi Bioinformatics 0 09-22-2011 10:26 AM

Reply
 
Thread Tools
Old 10-28-2016, 06:59 AM   #1
binfoUser
Member
 
Location: Portugal

Join Date: Jan 2016
Posts: 22
Default Software to annotate variants

I am wondering if there is any software that annotates variants not by the variants genomic coordinates but by their position in the cDNA.

Thank you
binfoUser is offline   Reply With Quote
Old 10-28-2016, 07:18 AM   #2
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 503
Default

If you use the transcriptome for your reference instead of the genome, then yes.
HESmith is offline   Reply With Quote
Old 10-28-2016, 08:05 AM   #3
binfoUser
Member
 
Location: Portugal

Join Date: Jan 2016
Posts: 22
Default

Do you mean the reference used to find the variants in the sequence? Or the reference used by the annotation software?
binfoUser is offline   Reply With Quote
Old 10-28-2016, 08:11 AM   #4
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 503
Default

Both: the alignment and annotation references have to match. But your original question implied that you had already determined variant positions by cDNA coordinates. Was that not correct?

If your intended question was "how do I determine the positions of variants in cDNAs?", that's standard output for most variant annotating software. The genome is reference, and gene annotation tables (refGene or GFF3) are used to identify those variants contained within coding sequences.

Last edited by HESmith; 10-28-2016 at 08:19 AM.
HESmith is offline   Reply With Quote
Old 10-28-2016, 08:17 AM   #5
binfoUser
Member
 
Location: Portugal

Join Date: Jan 2016
Posts: 22
Default

But I only have the file with the variants already identified, nothing else. And due to the nomenclature, some variants can't be annotated by their genomic coordinates.
binfoUser is offline   Reply With Quote
Old 10-28-2016, 08:22 AM   #6
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 503
Default

How were your variants identified (i.e., what was the software pipeline)? And what format are they in? (posting ~10 lines would be useful)
HESmith is offline   Reply With Quote
Old 10-28-2016, 08:34 AM   #7
binfoUser
Member
 
Location: Portugal

Join Date: Jan 2016
Posts: 22
Default

I don't know the pipeline used to identify the variants. The only thing that I have access to is the reference file used, that was: hg38.fa
The variants are saved in a VCF file. What I want to do is to annotate the variants, but some variants do not match the genomic coordinate (when the variants involve more than one nucleotide), and in that case using a software that annotates by genomic coordinate will not perform a correct annotation.
binfoUser is offline   Reply With Quote
Old 10-28-2016, 08:41 AM   #8
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 503
Default

If hg38 was the reference used for alignment and variant calling, then the variants in your VCF have genomic (not cDNA) coordinates. Is that not true? And most variant annotation software can accommodate multi-nucleotide variants, so your question/concern is unclear.

Please post an example of a variant from your VCF with more than one nucleotide.
HESmith is offline   Reply With Quote
Old 10-28-2016, 09:14 AM   #9
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,975
Default

Quote:
but some variants do not match the genomic coordinate (when the variants involve more than one nucleotide)
Then you may have a problem. You should go back and ask for whoever did the analysis for you for the reference they used.
GenoMax is offline   Reply With Quote
Reply

Tags
annotation, bioinformatics, software, variants

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:34 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO