SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
pileup file format Hena Bioinformatics 0 08-03-2011 03:30 AM
samtools pileup format foxyg Bioinformatics 3 11-16-2010 07:25 AM
pileup format- what is ^F EHC Genomic Resequencing 0 07-29-2010 12:01 PM
PubMed: The Effects of Alignment Quality, Distance Calculation Method, Sequence Filte Newsbot! Literature Watch 0 07-16-2010 02:00 AM
Coverage calculation (on GA data) marlei Bioinformatics 2 06-03-2010 09:44 AM

Reply
 
Thread Tools
Old 02-01-2012, 12:02 AM   #1
Lisamjb
Junior Member
 
Location: Melbourne

Join Date: Jan 2012
Posts: 1
Default Synonymous vs. non-synonymous mutations in pileup data

Hi!
Does anyone know of any program that can identify synonymous and non-synonymous mutations for population data in pileup format? I'm particularly interested in calculating pi(a)/pi(s). SAM format is also okay too, but I need something that can deal with Ns.
Thanks in advance for your help!

Last edited by Lisamjb; 02-01-2012 at 12:22 AM.
Lisamjb is offline   Reply With Quote
Old 02-01-2012, 12:57 PM   #2
Dameon
Member
 
Location: St. Louis, MO - USA

Join Date: Dec 2011
Posts: 14
Default

snpEff will identify synonymous and non-synonymous mutations for SNP data in pileup format. I am not sure how it will perform with population data though.
Dameon 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 10:14 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO