Snp-Annotation And Effect Prediction

Question

[jackuser1979]

I have mapped RNA-seq illumina paired-end reads to reference genome contigs(which is assembled contigs/scaffolds). I have VCF file called from variant caller, which consists of contigs (not by chromosome name). I tried running snpEff to human -GRCH37.64 which gives annotated gene list but not effect prediction.How can we use snpEff for contigs for variant annotation and effect prediction?

Answer 1

[Zev.Kronenberg]

Reading between the lines makes me think that you are working on a non-model organism. You need an annotation file (GFF3 ect) to tell the annotation tools where the genes/exons/cds are.

[jackuser1979]

My reference genome is the result of assembled contigs/scaffolds in which our lab working on. I am trying to find SNPs mapping subset of illumina paired-end reads to that assembled contigs. I found SNPs/contig. How can I proceed further?

[Zev.Kronenberg]

1) You need to define the goals of your project. 2) Find papers where they have done analyses similar to those your are interested in doing. Read their methods.

Answer 2

[Christian]

You could use CooVar to do that. It was specifically designed to work with non-model organisms.

CooVar: Co-occurring variant analyzer

BMC Research Notes 2012, 5:615

Disclaimer: I am co-author of this tool.

Answer 3

[mulin0424.li]

Here is a web-based tool for SNP annotation, visualization and effect prediction. Please visit http://jjwanglab.org/snvrap