Question: Annotation of Rat WGS data by AnnoVar
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gravatar for syrup16g_TO
4.5 years ago by
syrup16g_TO40
Japan
syrup16g_TO40 wrote:

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.

snp annotation genome • 1.6k views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 4.5 years ago by syrup16g_TO40

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

ADD REPLYlink written 4.5 years ago by Ashutosh Pandey11k
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