GATK DepthOfCoverage at high depth

lletourn · 08-13-2011, 07:31 AM

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 · 08-13-2011, 07:51 AM

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.

spreeth84 · 03-28-2012, 08:51 AM

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!

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
minimum depth variant calling samtools/gatk	m_elena_bioinfo	Bioinformatics	1	12-06-2011 09:31 AM
GATK / DepthofCoverage	nguyendofx	Bioinformatics	0	11-07-2011 11:21 AM
GATK - DepthOfCoverage	giverny	Bioinformatics	2	09-14-2011 02:48 PM
depth of coverage outputs gatk	m_elena_bioinfo	Bioinformatics	0	09-07-2011 03:58 AM
GATK depthofcoverage	foxyg	Bioinformatics	1	08-21-2010 10:22 AM

08-13-2011, 07:31 AM	#1
lletourn Member Location: Montreal Join Date: Oct 2009 Posts: 63	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

08-13-2011, 07:51 AM	#2
lletourn Member Location: Montreal Join Date: Oct 2009 Posts: 63	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.

03-28-2012, 08:51 AM	#3
spreeth84 Junior Member Location: Boston Join Date: Jan 2011 Posts: 9	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!