SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to deal with extremely unbalanced coverage in pooled sequencing data? Jiafen Bioinformatics 0 11-07-2012 01:42 PM
extra high coverage regions in exome sequencing data lyz1030 Bioinformatics 1 10-22-2012 03:26 AM
Agilent SureSelect - coverage of high GC regions NGSfan Genomic Resequencing 28 11-07-2011 02:13 PM
Extremely high cy3 signals chenglei SOLiD 3 10-05-2011 08:14 AM
downsampling high coverage regions in SAGs novi Bioinformatics 0 06-30-2011 02:28 AM

Reply
 
Thread Tools
Old 01-10-2013, 03:56 AM   #1
JMFA
Member
 
Location: Portugal

Join Date: Nov 2010
Posts: 11
Default Extremely high Coverage in some regions

Dear all,

I am currently working with NGS data for one individual sequenced using Illumina HiSeq 2000 (13-16x coverage).
I follow some standard pipelines to align and prepare the data for variant calling (BWA, Picard and GATK). (I am not interested in exome analysis but I've followed this pipeline to prepare the BAM files http://seqanswers.com/wiki/How-to/exome_analysis)

When I was ready for the calling step I decided to check the coverage of this individual using BEDTools. The average coverage looks good (14/15X) but in some regions I get extremely high values like 9200x or higher !

I don't think that this is normal and I believe that these values are not OK even for repetitive regions...

Do you have any idea of what might be wrong?
Thank you all in advance,
J
JMFA is offline   Reply With Quote
Old 01-10-2013, 10:30 PM   #2
cwhelan
Member
 
Location: Cambridge, MA

Join Date: Nov 2010
Posts: 23
Default

This is normal although it should only happen in a few regions. This paper suggests that it is due to misassembled regions of the reference where there should be many copies of a repeat but there's only one in the assembly:

http://bioinformatics.oxfordjournals...rmatics.btr354

You could check the BED files linked to from that paper to see if they match up with your high peaks.
cwhelan is offline   Reply With Quote
Old 01-11-2013, 03:42 AM   #3
JMFA
Member
 
Location: Portugal

Join Date: Nov 2010
Posts: 11
Default

Dear cwhelan,

Thanks for the reply!
Yes! Maybe its normal because I only get a few strange peaks.

Thanks again,
J
JMFA is offline   Reply With Quote
Reply

Tags
coverage, illumina, ngs, pipeline

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 03:03 AM.


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