Camilo

Thanks for the answers.

Thanks for the answers, they are very helpful. I have a final question, though. Is there a way to check why a possible variant is not being called by LoFreq?

I'm running lofreq call to call the variants, not lofreq somatic, and since I'm using human samples, according to the online documentation I should be using -s (source quality) in combination with -S.

Hello, I'm using LoFreq to call variants on some human tumor samples. We had analized those samples beforehand, so I had an idea about which variants should be called. The samples had some variants reported on dbSNP and according to the recommendations in the home page I decided to enable the -s flag and use -S with a dbSNP VCF file, however, those variants weren't being called. So, I've been wanting to ask: Does the -S option mask/remove the variants on the positions on the file?