Snp-Annotation And Effect Prediction

Question: Snp-Annotation And Effect Prediction

8.4 years ago by

jackuser1979 • 880

jackuser1979 • 880 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

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modified 7.7 years ago by mulin0424.li • 120 • written 8.4 years ago by jackuser1979 • 880

8.4 years ago by

Zev.Kronenberg ♦ 11k

United States

Zev.Kronenberg ♦ 11k 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 COMMENT • link written 8.4 years ago by Zev.Kronenberg ♦ 11k

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 REPLY • link written 8.4 years ago by jackuser1979 • 880

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 REPLY • link written 8.4 years ago by Zev.Kronenberg ♦ 11k

8.4 years ago by

Christian • 3.0k

Cambridge, US

Christian • 3.0k 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 COMMENT • link written 8.4 years ago by Christian • 3.0k

7.7 years ago by

mulin0424.li • 120

United States

mulin0424.li • 120 wrote:

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

ADD COMMENT • link written 7.7 years ago by mulin0424.li • 120

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