SNP annotation tool

Question

[mlscmahe]

I have list of SNPs from a GWAS study. I would like to know tools to annotate SNP with RSID (without strand information).

I need information like the nearest gene to which SNP belong or exist and region information like intronic/intergenic etc.

I will appreciate if somebody suggests appropriate tool for this purpose.

Answer 1

[Emily]

Have you looked at the Ensembl Variant Effect Predictor. You can use it as an online tool, or as a standalone perl script. You can input your list of IDs and it will give you the genomic coordinates, the genes/transcripts they hit or are near to, how they affect the genes in SO terms with amino acid changes and (optional) SIFT and PolyPhen scores where relevant, regulatory regions they hit, frequency data from 1000 genomes - there are in fact loads of options. I also have a BioStar Ad with more information.

Answer 2

[Björn]

Hi,

Try Annovar or snpeff.

Cheers,
Bjoern

[Dataman]

This is the working link for Annovar: http://annovar.openbioinformatics.org/en/latest/.

Answer 3

[Haluk]

SnpEff

Answer 4

[mlscmahe]

Thanks for all the suggestions. I found VariWatch as best one. I simply loved it.

Answer 5

[Collin]

You could try opencravat, which is available through a website, command line tool, or a local graphical interface.

Answer 6

[ff.cc.cc]

Hi, I usually filter snps from exome data with Exomiser in conjunction with or as alternative to annovar.

Sometimes also wannovar (a web interface to a annovar online server) revealed helpful

[psmirin]

Hi

I downloaded the Exomiser and tried to use for the first time , and I am running the following command line:

java -Xms5g \
  -Xmx5g \
  -jar /exomiser-cli-4.0.0/exomiser-cli-4.0.0.jar \
  --prioritiser=phenix \
  -v 278.vcf \
  -I AR \
  -E human \
  -f VCF \
  -F 1 \
  --hpo-ids HP:0006349,HP:0001249,HP:0006349

but I keep getting an error :

2014-10-05 15:55:39,270 WARN  de.charite.compbio.exomiser.core.filter.FrequencyFilter [main] - chr1:g.13958C>- frequency data has not been set - Frequency filter failed.

Any suggestions?

Thank you for your help

Answer 7

[deanna.church]

Try the NCBI variation reporter.