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Old 01-12-2014, 05:22 PM   #1
Location: Washington DC

Join Date: Sep 2011
Posts: 10
Default GATK depthofCoverage for SOLiD data


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
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.
ahli1981 is offline   Reply With Quote
Old 01-13-2014, 03:45 AM   #2
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Location: Budapest

Join Date: Mar 2010
Posts: 329

Try -allowPotentiallyMisencodedQuals
TiborNagy is offline   Reply With Quote

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