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?
•
written
by
jackuser1979
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.
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?
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.
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.
Here is a web-based tool for SNP annotation, visualization and effect prediction. Please visit http://jjwanglab.org/snvrap
Log in to answer this question.
