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Old 11-24-2011, 08:23 PM   #1
wanguan2000
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Location: shanghai

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Default 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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