SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
minimum depth variant calling samtools/gatk m_elena_bioinfo Bioinformatics 1 12-06-2011 08:31 AM
GATK / DepthofCoverage nguyendofx Bioinformatics 0 11-07-2011 10:21 AM
GATK - DepthOfCoverage giverny Bioinformatics 2 09-14-2011 01:48 PM
depth of coverage outputs gatk m_elena_bioinfo Bioinformatics 0 09-07-2011 02:58 AM
GATK depthofcoverage foxyg Bioinformatics 1 08-21-2010 09:22 AM

Reply
 
Thread Tools
Old 08-13-2011, 06:31 AM   #1
lletourn
Member
 
Location: Montreal

Join Date: Oct 2009
Posts: 63
Default GATK DepthOfCoverage at high depth

I have a sample on which custom capture was done. Many of the baits have >2000x coverage.

When running DepthOfCoverage initially I never saw values >500x but then noticed I forgot to set the bins bigger. I set them at 20,000 just to be safe, now no values go over 1000...I really don't get why.
I even set a summaryCoverageThreshold at 1200 and it's always 0.

With genome browser I can clearly see some baits at >2000 even some at 5000.

Any ideas

Here's the command:
Code:
java -jar /data/solexa/aligners/GenomeAnalysisTK-1.0.5777/GenomeAnalysisTK.jar -T DepthOfCoverage -R human_hg19.fasta -I sample.bam -o sample.targetCoverage -L all.interval_list --minMappingQuality 15 --minBaseQuality 10 --omitDepthOutputAtEachBase --logging_level ERROR --summaryCoverageThreshold 30 --summaryCoverageThreshold 50 --summaryCoverageThreshold 200 --summaryCoverageThreshold 500 --summaryCoverageThreshold 700 --summaryCoverageThreshold 1000 --summaryCoverageThreshold 1200 --summaryCoverageThreshold 2000 --start 1 --stop 20000 --nBins 19999
lletourn is offline   Reply With Quote
Old 08-13-2011, 06:51 AM   #2
lletourn
Member
 
Location: Montreal

Join Date: Oct 2009
Posts: 63
Default

I finally found my answer.

By default GATK downsamples by sample. The downsampling coverage is...drum roll...1000.

To fix this set the number of bins *AND* set -dt NONE

Why one would downsample when computing coverage is beyond me.
lletourn is offline   Reply With Quote
Old 03-28-2012, 07:51 AM   #3
spreeth84
Junior Member
 
Location: Boston

Join Date: Jan 2011
Posts: 9
Default

Thanks! looks like this also happens in the Unified Genotyper in reporting the AD and DP numbers. I was struggling to explain why the DP did not match the coverage at the position and if the quality filters were being too stringent!
spreeth84 is offline   Reply With Quote
Reply

Tags
coverage, coverage calculation, gatk, gatk depthofcoverage

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 04:59 PM.


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