annovar output - question

[dkrtndhkd]

I run annovar to annotate my snp file.

I saw this message:

WARNING: A total of 273 sequences will be ignored due to lack of correct ORF annotation

somebody please let me know what's the meaning?

[Heisman]

I'm pretty sure that's in reference to sequences it loads from its own databases; nothing to do with your samples. I wouldn't worry about it.

[dkrtndhkd]

Thank you

and futher question...

the word 'ignored' means that Annovar didn't annotate any gene name and just deleted the SNP??

[Heisman]

I can't remember off the top of my head. Could you copy and paste the text where it says "ignored" (and if it's associated with a specific input line, copy and paste that as well).