Question: RNA-seq SNP analysis
0
gravatar for sbombin
3.1 years ago by
sbombin10
sbombin10 wrote:

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.

ADD COMMENTlink modified 3.0 years ago by Charles Warden6.8k • written 3.1 years ago by sbombin10
2
gravatar for igor
3.1 years ago by
igor7.7k
United States
igor7.7k wrote:

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

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

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by igor7.7k
2
gravatar for ivivek_ngs
3.1 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

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.
ADD COMMENTlink written 3.1 years ago by ivivek_ngs4.8k
1
gravatar for Charles Warden
3.0 years ago by
Charles Warden6.8k
Duarte, CA
Charles Warden6.8k wrote:

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

ADD COMMENTlink written 3.0 years ago by Charles Warden6.8k
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