Thread: Gatk vqsr
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Old 02-19-2014, 07:25 AM   #4
grakocevic
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Location: Belgrade

Join Date: Feb 2014
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You should check the Filter column in the VCF.
Filtering variants in a VCF usually doesn't mean deleting them, but rather writing something in that column.
Anything that is not '.' or 'PASS' typically means that the variant is filtered, and many tools will actually disregard all such variants.

If really you want to remove the filtered variants you can use GATK SelectVaraints and set it to exclude filtered...
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