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

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Default SNP annotation

Hi
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 convert2annovar.pl option, and it looks fine.

In order to make my own annotation database I created gff3 file of the reference genome (GenBank file) using bp_genbank2gff3.pl BioPerl script and also validated it using an online gff3 validator available at http://modencode.oicr.on.ca/cgi-bin/...te_gff3_online. The gff3 file looks perfect. Please suggest how to use this gff file for annotation in ANNOVAR.

Thanks
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Old 02-28-2014, 11:17 AM   #2
sytiger
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Default

I would like to know too.

Any one could give a hint?

Thanks
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