SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
target region file for samtools (.bed file) lifetech01 Bioinformatics 1 07-09-2014 03:59 PM
Exome Sequencing vs Target Region Sequencing Marco0208 Genomic Resequencing 4 11-25-2013 10:09 PM
Bait tiling snapper Sample Prep / Library Generation 2 06-05-2012 10:31 PM
SureSelect bait QC via RNA-seq ? ECO Sample Prep / Library Generation 1 05-22-2012 11:04 AM
Zygosity difference oyvindbusk Bioinformatics 3 01-31-2012 05:56 AM

Reply
 
Thread Tools
Old 01-21-2013, 01:27 AM   #1
Brambo
Junior Member
 
Location: Belgium

Join Date: Dec 2012
Posts: 3
Default Difference between bait and target region

Hi all,

I am using CalculateHsMetrics.jar of PicardTools.
Although I defined my targetinterval exactly the same as my bait interval (BAIT_INTERVALS=$targetInterval TARGET_INTERVALS=$targetInterval), my mean_bait_coverage and mean_target_coverage in my output file do differ ( 600X vs 2X) What can be the reason for this?

thanks in advance,
Brambo is offline   Reply With Quote
Old 10-08-2015, 07:56 AM   #2
david_2012
Junior Member
 
Location: Germany

Join Date: Mar 2012
Posts: 4
Default

Wondered the same thing and found your post DuckDuckGoing it. Eventually figured out the little difference in how they are computed, according to the documentation (http://broadinstitute.github.io/pica...ml#HsMetrics):
MEAN_BAIT_COVERAGE The mean coverage of all baits in the experiment.
MEAN_TARGET_COVERAGE The mean coverage of targets that received at least coverage depth = 2 at one base.

I think the difference is that the mean target coverage is only calculated for targets where at least one base has a coverage of 2 or higher. However, mean bait coverage is calculated for ALL baits, including those with no coverage at all. You would thus expect these (almost) no coverage baits to drag down the average to a lower value, which is what I see.
david_2012 is offline   Reply With Quote
Reply

Tags
bait, interval, picard, target

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 08:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO