The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?