What is the difference between Phred and GQ(Genotype quality)? 
Which are the values for a good cut-off?


Phred scale is usually used for representing the base error probability in lograrithm format:

$Phred score = -10 log_10 error probability$

genotype quality is how certian the genotype calling algorithm is about the genotype called. It is usually displayed in 10*log(relative_score_of_genotype) format too.