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-   -   Deleterious information in dbSNP (http://seqanswers.com/forums/showthread.php?t=21643)

genelab 07-12-2012 07:11 PM

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!

ymc 07-12-2012 07:15 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 09:08 PM

Quote:

Originally Posted by ymc (Post 78765)
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 01:50 AM

Quote:

Originally Posted by genelab (Post 78767)
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 10:31 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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