Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK Base Quality Recalibration ashuchawla Bioinformatics 5 02-09-2012 11:12 AM
GATK: Base quality score recalibration fabrice Bioinformatics 2 11-05-2011 04:54 AM
GATK base quality recalibration suppose to keep old and new quality scores? Heisman Bioinformatics 2 10-21-2011 08:40 AM
Quality recalibration Nick Bioinformatics 0 06-30-2010 01:07 PM
recalibration using second base call for Illumina drio Bioinformatics 1 03-04-2010 05:24 PM

Thread Tools
Old 06-24-2010, 02:05 PM   #1
Location: canada

Join Date: May 2010
Posts: 16
Default Base quality recalibration

Can someone explain the basic idea behind quality recalibration and how it is corrected?

I realize that the sequencing platform has difficulty in base calling for the bases near the late cycles (due to phasing or cluster overlap). A naive way to correct for this is to simply find out the mean drop in base quality between adjacent bases and then add this differential to read. This approach is flawed as the drop in quality could be due to reasons I am unaware of but might be independent of the detection problem mentioned earlier.

So the idea is that one can use information from (local re)alignment to improve the quality of the base call. I actually don't understand this latter strategy. What I am guessing is that if the read aligns very well to the reference, but for some reason the quality score of some base is much lower than the average quality of overall read -- suggesting then it might be justified to increase the confidence in the quality of the position.

I saw a plot in the GATK documents that after recalibration the expected and the observed quality aligns much better (at the diagonal) but I don't understand how the expected quality information was obtained.

Thanks in advance
christophpale is offline   Reply With Quote

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 11:40 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO