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Old 08-13-2011, 07:31 AM   #1
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:
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
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Old 08-13-2011, 07:51 AM   #2
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.
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Old 03-28-2012, 08:51 AM   #3
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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!
spreeth84 is offline   Reply With Quote

coverage, coverage calculation, gatk, gatk depthofcoverage

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