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Old 01-12-2014, 06:22 PM   #1
ahli1981
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Location: Washington DC

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Default GATK depthofCoverage for SOLiD data

Hi,

Anybody know how to use GATK depthofcoverage on SOLiD bam? The bam has already been calibrated but GATK detects very high quality score, considers it as encoding error and aborts.

I tried to use
-fixMisencodedQuals
but still cannot get through GATK depthofcoverage, because GATK thinks the bam is a mixture of reads with error encoding quality and correct encoding quality......

Thanks in advance.
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Old 01-13-2014, 04:45 AM   #2
TiborNagy
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Try -allowPotentiallyMisencodedQuals
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