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Test-drive the GATK tools and Best Practices pipelines on Terra
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QUAL field value of VCF files after VQSR
I saw "LowQual" in the QUAL field of some records in VCF files which has been VQSR. I wonder whether these records have ever been used in the VQSR. If they have been used in that step, but without tagging something like "VQSRTrancheSNP99.90to100.00", does it mean that they are somehow ok in terms of VQSR?