strand-bias settings

[mortunco]

Hi,

I am using strelka 2.8.0 in somatic variant calling workflow and something confused me so.

version 2.9.0 configureStrelkaSomaticWorkflow.py strand bias is reporting as follows. ( this is same in 2.8.0)

#
# Fraction of snv noise attributed to strand-bias.
#
# It is not recommended to change this setting. However, if it is
# essential to turn the strand bias penalization off, the following is
# recommended:
# Assuming the current value of ssnvNoiseStrandBiasFrac is 0.5,
# (1) set ssnvNoiseStrandBiasFrac = 0
# (2) divide the current ssnvNoise value by 2
#
ssnvNoiseStrandBiasFrac = 0.0

and ssnvNoise is --> ssnvNoise = 0.0000000005

So my question is as follows.

1. given used ssnvNoiseStrandBiasFraction value was supposed to be .5 but it is actually set to 0.0. what is the default ssnvNoise value? Is the ssnvNoie value on top is the halfed value or is(ssnvNoise = 0.0000000005) it the actually one ?

Also could you help me to figure out how SNVBS value calculated in the vcfs?

Thank you very much for your help,

T.

[GeorgetteTanner]

Hi

I'm also wondering about this. Has anyone been able to find out what the recommended ssnvNoiseStrandBiasFraction value is?

Thanks!