SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Why MAQ consensus seq better than SAMtools consensus ?? av_d Genomic Resequencing 5 10-18-2015 04:44 AM
Extracting REF and ALT from VCF kasthuri Bioinformatics 5 05-24-2013 07:00 AM
merge-vcf yielding '.' for ALT nikkiat Bioinformatics 0 04-20-2012 08:48 AM
bacterial consensus sequence reference guided assembly Kerensa Bioinformatics 0 01-10-2011 09:38 PM
alt promoter use - Output from Cufflinks nat Bioinformatics 0 09-06-2010 01:52 AM

Reply
 
Thread Tools
Old 11-13-2013, 10:19 AM   #1
jmartin
Member
 
Location: St. Louis

Join Date: Dec 2009
Posts: 74
Default Ref.-guided consensus using alt. alleles

I've recently used samtools mpileup to generate a reference guided consensus sequence of my data. But the consensus includes IUPAC degenerate characters to represent sites of variation. What I'd like to do is to generate the same consensus, but reporting the 'alternate' allele (the allele from my data) at each of those sites.

Is there an easy way to do this already out there? I can see how I could script something up that would use the vcf to get this done, but I don't want to re-invent the wheel if something can already do this.
jmartin is offline   Reply With Quote
Reply

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 07:12 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO