RNA-seq SNP analysis

Question

[sbombin]

Hello,

I generated VCF and .bam files from transcriptomes files of C.remanei. Now, I want to do some functional annotation of SNPs or some other analyses to begin with. I am actually very new to all these analyses and not sure what is the best way start with. I found some publications with usinf GWAS database but I am not sure if I could use it with C.remanei. Also, I found some information about VariantsToTable on GATK website but it looks like this tool makes only the table of all SNPs and do not perform functional annotation. All other functional annotations tools that I found ask about SNP IDs, which I do not have because there is no dbSNP file for C.remanei. Could you please advise what is the best way to start variants analyses with VCF and bam files?

Thank you.

Answer 1

[igor]

There are a few tools available for variant annotation. For example:

• ANNOVAR -http://annovar.openbioinformatics.org/en/latest/
• SnpEff - http://snpeff.sourceforge.net/
• vcfanno - https://github.com/brentp/vcfanno

Also, see previous discussion here: What Is The Best Tool For Mouse (Mm9 Or Mm10) Variant Annotations?

Answer 2

[ivivek_ngs]

I think once should also take a look at :

1. VEP

2. Try to take a look at Ensemble Metazoa

3. Wormbase and see how to use it for your work.

Answer 3

[Charles Warden]

You might have problems using ANNOVAR on a non-model organism, but SNPeff should be OK.

Looks like VEP will work with C. elegans, but you probably can't use that (unless you aligned to the C. elegans genome instead of a C.remanei genome).

Also, did you use a pipeline for calling variants that considers RNA-Seq data? For example, GATK has a modified pipeline for RNA-Seq data: https://www.broadinstitute.org/gatk/guide/article?id=3891

I would also ask if you were filtering out known RNA-editing events, but that may not be possible with your sample. However, you can also check the mutation type frequencies to make sure you don't have over-representation of A-to-G mutations.

I'm not really a worm guy, but if you are willing to use C. elegans RNA-editing events (which is probably OK), I found this paper that provides a list of sites in the supplemental materials (which you could liftOver to your genome, if needed): http://www.ncbi.nlm.nih.gov/pubmed/25373143