Hello,
I'm new to this forum and bioinformatics for that matter.
I'm studying functional genomics and ecology of hybridization in flying squirrels, with the goal of identifying SNPs between two flying squirrel species, and profiling hybrid individuals based on a handful of those variable markers.
I've de novo assembled a flying squirrel transcriptome with Trinity, and have called SNPs using the SAMtools variant calling pipeline (mpileup etc).
I now would like to use ANNOVAR to annotate the SNPs that SAMtools has called. ANNOVAR provides detailed documentation on annotating SNPs based of human genomic databases. I believe that the closest open-source annotated genome to my study species in the thirteen-lined ground squirrel (SpeTri2), followed by the mouse (mm9).
I'm confused as to what databases from the SpeTri2 annotated assembly I should be downloading and using in ANNOVAR, as I noticed that in the ANNOVAR quick-start guide, the directions called for many human genomic databases.
Any info would be great.
Cheers.
I'm new to this forum and bioinformatics for that matter.
I'm studying functional genomics and ecology of hybridization in flying squirrels, with the goal of identifying SNPs between two flying squirrel species, and profiling hybrid individuals based on a handful of those variable markers.
I've de novo assembled a flying squirrel transcriptome with Trinity, and have called SNPs using the SAMtools variant calling pipeline (mpileup etc).
I now would like to use ANNOVAR to annotate the SNPs that SAMtools has called. ANNOVAR provides detailed documentation on annotating SNPs based of human genomic databases. I believe that the closest open-source annotated genome to my study species in the thirteen-lined ground squirrel (SpeTri2), followed by the mouse (mm9).
I'm confused as to what databases from the SpeTri2 annotated assembly I should be downloading and using in ANNOVAR, as I noticed that in the ANNOVAR quick-start guide, the directions called for many human genomic databases.
Any info would be great.
Cheers.
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