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11-24-2011, 09:23 PM
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Member
Location: shanghai Join Date: Nov 2010
Posts: 24
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GATK snp calling
The number of LowQual using ApplyRecalibration as the same as the LowQual in raw.vcf.
LowQual number does not change!!! and a little PASS change to TruthSensitivityTranche99.00to99.90. should I filtering itself based on the VQSLOD values? I followed the pipeline: http://www.broadinstitute.org/gsa/wi...th_the_GATK_v3 |
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