Snp-Annotation And Effect Prediction
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9.6 years ago
jackuser1979 ▴ 890

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?.

bioinformatics vcf • 4.0k views
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9.6 years ago

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.

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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?

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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.

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9.6 years ago
Christian ★ 3.0k

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.

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8.9 years ago
mulin0424.li ▴ 120

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

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