The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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.