HI, my mouse variant data (VCF format) has been processed by recalibrating, snp calling and filtering by GATK package.
Now it is time to annotate this variant data by ANNOVAR package. I processed it as follows,
1) convert the VCF file format to the annovar file format:
$convert2annovar.pl --format vcf4 --includeinfo snps.filtered.vcf > snps.annovar &
2) I have one package - mouse mm10 annotation package that is downloaded from Illumina resource ( based on UCSC March 6, 2013)
This package contains 3 different files including "Genes file" which is consisted of ChromInfo.txt, genes.gtf,refFlat.txt.gz,refGene.txt and refSquSummary.txt, "Small RNA file" includes mature.fa and precursor.fa and "variation file " has snp137.txt.gz.
From an example of using annovar in human the command is like this:
[kai@beta ~/]$ annotate_variation.pl ex1.human -buildver hg19 humandb/
(copied and modified from http://www.openbioinformatics.org/annovar/annovar_gene.html)
For the mouse variants annotation, I was totally lost now, my questions are
1) My annotation in my computer seems a little bit complex, which one I use? or use just the whole package? To make my analysis straight forward, Where to download the mm10 annotation data WHICH works EXACTLY for annotation of ANNOVAR?
2) What is the correct or PERTINENT commands for my mouse exome annotation by ANNOVAR? ( the example above for human is obviously not for my mouse data)