Test-drive the GATK tools and Best Practices pipelines on Terra
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VQSLOD score and variant quality
Dear GATK team,
For VQSLOD score, can I understand it as way to rank variants. The higher the score, the more reliable the variant being true positive?
I have an output file from GATK 2, and there are some variants with low VQSLOD scores (e.g. -5), and being labeled as "Pass", while some other variants with higher VQSLOD scores being labeled as "VQSRTrancheSNP99.90to100.00". Do these results make sense to you?
Please let me know.