I have seen a issue that one of the variant which is important in my analysis in filtered out as HighSNVSB;NoPassedVariantGTs having score above 300. Although I can see that it is present in IGV
There is another variant filtered out with same reason but it is not visible in IGV and have score of 20
It is happening in many files. I work with rare disorders so many variants are rare.
Kind guide me to retain variant with high score.
I have used the following methods
ssnvPrior = 0.0001
sindelPrior = 0.000001
ssnvNoise = 0.0000000005
sindelNoiseFactor = 2.2
ssnvNoiseStrandBiasFrac = 1 and 0.0 and 0.5 ### nothing works <---
Hi,
I have seen a issue that one of the variant which is important in my analysis in filtered out as HighSNVSB;NoPassedVariantGTs having score above 300. Although I can see that it is present in IGV
There is another variant filtered out with same reason but it is not visible in IGV and have score of 20
It is happening in many files. I work with rare disorders so many variants are rare.
Kind guide me to retain variant with high score.
I have used the following methods
ssnvPrior = 0.0001
sindelPrior = 0.000001
ssnvNoise = 0.0000000005
sindelNoiseFactor = 2.2
ssnvNoiseStrandBiasFrac = 1 and 0.0 and 0.5 ### nothing works <---