Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
VCF SNP Annotation ashkot Bioinformatics 4 07-16-2012 12:37 PM
annotation file for maq snp calling johnsequence Bioinformatics 0 10-26-2011 11:39 AM
snp annotation elisadouzi Bioinformatics 1 04-22-2011 10:31 AM
eagleview and snp annotation litali Bioinformatics 0 07-20-2010 05:02 AM
Is there any package available for SNP/Indel annotation? Ling Bioinformatics 3 01-28-2010 09:58 AM

Thread Tools
Old 04-11-2012, 01:54 PM   #1
Location: USA

Join Date: Apr 2012
Posts: 12
Default SNP annotation

What is the best and easy way of annotating SNPs/InDels if reference genome of the organism is not available through UCSC genome browser? I have a list of SNPs and InDels generated using BWA-GATK in VCF format from the bacteria Staphylococcus aureus. I am trying to annotate them (location of these SNPs in context of reference genome) using ANNOVAR. I have converted this VCF file into the annovar format using option, and it looks fine.

In order to make my own annotation database I created gff3 file of the reference genome (GenBank file) using BioPerl script and also validated it using an online gff3 validator available at The gff3 file looks perfect. Please suggest how to use this gff file for annotation in ANNOVAR.

baika is offline   Reply With Quote
Old 02-28-2014, 11:17 AM   #2
Junior Member
Location: Baltimore

Join Date: May 2013
Posts: 3

I would like to know too.

Any one could give a hint?

sytiger is offline   Reply With Quote


Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 09:39 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO