Question: Snp-Annotation And Effect Prediction
1
gravatar for jackuser1979
8.4 years ago by
jackuser1979880
US
jackuser1979880 wrote:

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?.

vcf bioinformatics • 3.7k views
ADD COMMENTlink modified 7.7 years ago by mulin0424.li120 • written 8.4 years ago by jackuser1979880
1
gravatar for Zev.Kronenberg
8.4 years ago by
United States
Zev.Kronenberg11k wrote:

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.

ADD COMMENTlink written 8.4 years ago by Zev.Kronenberg11k

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?

ADD REPLYlink written 8.4 years ago by jackuser1979880
1

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.

ADD REPLYlink written 8.4 years ago by Zev.Kronenberg11k
1
gravatar for Christian
8.4 years ago by
Christian3.0k
Cambridge, US
Christian3.0k wrote:

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.

ADD COMMENTlink written 8.4 years ago by Christian3.0k
0
gravatar for mulin0424.li
7.7 years ago by
mulin0424.li120
United States
mulin0424.li120 wrote:

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

ADD COMMENTlink written 7.7 years ago by mulin0424.li120
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