While running I occasionally get warning messages on some of my samples
"mafR not sufficiently small"
"mafR<0.09 in less than 10% genome"
Or
"possibly subclonal 2+2 states present"
"mafR larger than expected if -0.0970249266606138 is diploid level"
"not consistent for 1 copy loss from diploid in segclust: 21, 25, 26"
I'm pretty sure that there are subclonal copy number states in some of these samples, but I am no longer using the emcncf2 function which seemed to allow for that, as comments and issues said that it was unstable.
Additionally, I have played around a bit with the cval in procSample, and have had to significantly decrease the nhet value for some samples in order to get calls in certain areas of the genome.
My question is how to interpret these warning messages? If I receive them does that mean that I should continue tweak the cval or nhet values to produce a better fit, or accept that this may be the best I will get out of this sample?
Hello,
While running I occasionally get warning messages on some of my samples
"mafR not sufficiently small"
"mafR<0.09 in less than 10% genome"
Or
"possibly subclonal 2+2 states present" "mafR larger than expected if -0.0970249266606138 is diploid level" "not consistent for 1 copy loss from diploid in segclust: 21, 25, 26"
I'm pretty sure that there are subclonal copy number states in some of these samples, but I am no longer using the emcncf2 function which seemed to allow for that, as comments and issues said that it was unstable.
Additionally, I have played around a bit with the cval in procSample, and have had to significantly decrease the nhet value for some samples in order to get calls in certain areas of the genome.
My question is how to interpret these warning messages? If I receive them does that mean that I should continue tweak the cval or nhet values to produce a better fit, or accept that this may be the best I will get out of this sample?