Deleterious information in dbSNP

genelab · 07-12-2012, 08:11 PM

Hello everyone,
How could I obtain the SNPs which are deleterious in the dbSNP?

Is the recent versions of dbSNP containing the deleterious information if the SNP sites is deleterious?

Thanks a lot!

ymc · 07-12-2012, 08:15 PM

ftp://gsapubftp-anonymous@ftp.broadi...35.hg19.vcf.gz

SNPs with alternate allele shorter than the reference allele are deletions

genelab · 07-12-2012, 10:08 PM

Quote:

Originally Posted by ymc

ftp://gsapubftp-anonymous@ftp.broadi...35.hg19.vcf.gz

SNPs with alternate allele shorter than the reference allele are deletions

thanks for you reply~

my purpose is to obtain the deleterious snp sits.

Any body knows ?

Many thanks~

ymc · 07-13-2012, 02:50 AM

Quote:

Originally Posted by genelab

thanks for you reply~

my purpose is to obtain the deleterious snp sits.

Any body knows ?

Many thanks~

snp position is also in the vcf file

shyam_la · 07-13-2012, 11:31 AM

Based on my understanding of your question, do this:

Go to: http://www.ncbi.nlm.nih.gov/snp/limits

Choose organism and then under annotation, check "clinical/lsdb submissions" and also choose "pathogenic" and "probably pathogenic". Hit Search.

You can download it in a format you want using "display settings" on left top.

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07-12-2012, 08:11 PM	#1
genelab Member Location: honston Join Date: Nov 2009 Posts: 27	Deleterious information in dbSNP Hello everyone, How could I obtain the SNPs which are deleterious in the dbSNP? Is the recent versions of dbSNP containing the deleterious information if the SNP sites is deleterious? Thanks a lot!

07-12-2012, 08:15 PM	#2
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	ftp://gsapubftp-anonymous@ftp.broadi...35.hg19.vcf.gz SNPs with alternate allele shorter than the reference allele are deletions

07-13-2012, 11:31 AM	#5
shyam_la Member Location: California Join Date: Mar 2012 Posts: 97	Based on my understanding of your question, do this: Go to: http://www.ncbi.nlm.nih.gov/snp/limits Choose organism and then under annotation, check "clinical/lsdb submissions" and also choose "pathogenic" and "probably pathogenic". Hit Search. You can download it in a format you want using "display settings" on left top.