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We are doing WES on hundreds of samples and the average sequencing depth is 60X. I used the sensitivity 99.9% for the PASS filter in VQSR. Attached is the histagram of VQSLOD for around 900,000 SNPs with PASS filter and call rate > 95%. I wonder if you can help me with two questions?
1. is it normal to have half of the SNPs with VQSLOD < 0?
2. why so few SNPs around VQSLOD = 0?