How to analyze non-Human whole genome re-sequencing data?

Question

[syrup16g_TO]

Hi everyone,

We did whole-genome sequencing of a disease-model rat.

We mapped reads on Rat genome(rn5), and called variants(SNVs, indels, SVs).

But we don't know the following way to analyze variants data.

If sample were of human, we would annotate variants using DBs( 1000g, dbSNP, and so on,,,).

Please let me know a pipeline of analyzing non-Human WGS data.

Thank you.

Answer 1

[iraun]

If you want to annotate the snps you've detected I recommend you to use SnpEff. It is a very intuitive and user friendly genetic variant annotation and effect prediction tool. This tool supports about 20.000 genomes, including rat, so I think it could be a good start point.

[syrup16g_TO]

Very thanks, airan.

I used SnpEff, and felt it suitable for me.

[iraun]

You're welcome :-)