Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
MAQ SNP calling bioinfosm Bioinformatics 10 01-03-2012 01:03 AM
annotation file for maq snp calling johnsequence Bioinformatics 0 10-26-2011 11:39 AM
Any software for snp calling other than MAQ? ericfit Bioinformatics 1 01-21-2011 10:40 PM
MAQ vs BWA/SAMTools - differences in SNP calling algorithm? mard Bioinformatics 2 10-20-2010 03:17 PM
MAQ and SNP calling michy Bioinformatics 3 12-11-2009 09:23 AM

Thread Tools
Old 01-06-2010, 01:35 PM   #1
Location: california

Join Date: Jan 2010
Posts: 22
Default percentage of SNP calling in MAQ

How to show directly the percentage of SNP calling in the final.snp file generated from MAQ, that is, how many percent of ATGC in this final SNP report. Fox example, if A (reference) was changed to G (consensus), what is percentage of this G? At the position, maybe 80% of G, 18% of C, 1% of A, and 1% of T. Is there any column we can add in the final report to show these percentage number? Instead of running the MAQ view function that might create a couple hundred GB data, too big.
johnsequence is offline   Reply With Quote
Old 01-08-2010, 10:54 AM   #2
Senior Member
Location: Vancouver, Canada

Join Date: Feb 2008
Posts: 236

I'm currently working on the same problem - I'm not sure there's an answer. A similar question has also been posted to the Maq mailing list, and there doesn't seem to be a reply.

The more you know, the more you know you don't know. —Aristotle
apfejes is offline   Reply With Quote

maq snp

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 09:03 AM.

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