In Gene-based Annotation, there is mention that an accessory script coding_change.pl offers functionality to assess if a frameshift indel will cause a premature stop-gain codon and nonsense-mediated decay. If I then read Accessory Programs, there's no explanation of what the value would be if there was such an alteration. It looks like line14 is an example of such an indel, but its only annotation is "protein-altering". Also, if ANNOVAR actually does predict nonsense-mediated decay, which rule does it use? Is it the popular convention of at least 50 bases upstream of the last exon-exon junction?
In Gene-based Annotation, there is mention that an accessory script
coding_change.ploffers functionality to assess if a frameshift indel will cause a premature stop-gain codon and nonsense-mediated decay. If I then read Accessory Programs, there's no explanation of what the value would be if there was such an alteration. It looks like line14 is an example of such an indel, but its only annotation is "protein-altering". Also, if ANNOVAR actually does predict nonsense-mediated decay, which rule does it use? Is it the popular convention of at least 50 bases upstream of the last exon-exon junction?