Annotation of Rat WGS data by AnnoVar

Question

[syrup16g_TO]

I want to annotate Rat WGS data using AnnoVar software.

WGS reads are mapped to rn5 reference. Therefore, I tried to use rn5 annotation of AnnoVar databases, but failed.

How can I use rn5 annotation? Please let me know, thanks.

[Ashutosh Pandey]

You can either use SnpEff that may or may not have annotation for rn5. For both Annovar and SnpEff you can also build a annotation database using GFF/GTF file from UCSC or Ensembl, reference genome. Check this: http://snpeff.sourceforge.net/SnpEff_manual.html#databases