Question: SNP annotation tool
4
gravatar for mlscmahe
5.9 years ago by
mlscmahe80
Kuwait
mlscmahe80 wrote:

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.

snp annotation • 17k views
ADD COMMENTlink modified 19 months ago by zx87548.8k • written 5.9 years ago by mlscmahe80
4
gravatar for Emily_Ensembl
5.9 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

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 The Ensembl Vep For Easy Analysis Of Your Variants with more information.

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Emily_Ensembl20k
3
gravatar for Björn
5.9 years ago by
Björn650
Germany
Björn650 wrote:

Hi, try Annovar (http://www.openbioinformatics.org/annovar/) or snpeff (http://snpeff.sourceforge.net/).

Cheers,

Bjoern

ADD COMMENTlink written 5.9 years ago by Björn650
2
gravatar for Haluk
5.9 years ago by
Haluk170
Lincoln, Nebraska
Haluk170 wrote:

SnpEff

ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by Haluk170
1
gravatar for mlscmahe
5.9 years ago by
mlscmahe80
Kuwait
mlscmahe80 wrote:

Thanks for all the suggestions. I found VariWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/main.do) as best one. I simply loved it.

ADD COMMENTlink written 5.9 years ago by mlscmahe80
0
gravatar for ff.cc.cc
5.9 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

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

ADD COMMENTlink written 5.9 years ago by ff.cc.cc1.3k

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 suggestion ?

Thank you for your help

 

 

 

 

 

ADD REPLYlink written 5.2 years ago by psmirin0
0
gravatar for deanna.church
5.9 years ago by
deanna.church1.1k
Bethesda, MD
deanna.church1.1k wrote:

Try the NCBI variation reporter: http://www.ncbi.nlm.nih.gov/variation/tools/reporter

ADD COMMENTlink written 5.9 years ago by deanna.church1.1k
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