How Can I Obtain All Snp Rs#?

Question

[J.F.Jiang]

Hi all,

I want to obtain a set of all 1000G snps, without genotypes, but some basic information such as chr, pos.,alles and rs#

Should I use the dbsnp132_20101103.vcf.gz to get the dataset? If so, how can i process with it?

OR is there any existed such file to download?

Thanks!

[J.F.Jiang]

I can now extract all snps from the file I mentioned, AM I correct?

And if I want to use the specific population SNPs list, does it mean I could only use the HapMap DATA?

Answer 1

[Irsan]

Go to the table browser of UCSC Choose:

Clade: Mammal Genome: Human Assembly: hg19 Group: Variation and Repeats track: common SNPs (132) table: snp132common region: genome output format: BED (I prefer .bed ...) output file: snps_132.bed

click "get Output" click "get BED"

This is just a plain text file. You can open it in IGV, Excel 2007 (if less than 1.04 million rows), text editor, terminal, whatever you like ...

Dont know whats in your "dbsnp132_20101103.vcf.gz" but you can use gunzip to extract it (it is archived like a zip-file) and see whats inside (text editor, Excel, ...)

[J.F.Jiang]

the file I mentioned is here: ftp://ftp.1000genomes.ebi.ac.uk/../vol1/ftp/technical/reference/

and in UCSC browser, what's the difference between snp132 and 135?

[Irsan]

see http://genome.ucsc.edu/goldenPath/newsarch.html

10 February 2012 - dbSNP 135 Available for hg19

We are pleased to announce the release of four tracks derived from dbSNP build 135, available on the human assembly (GRCh37/hg19). dbSNP build 135 is available at NCBI. The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the Genome Browser.

As for dbSNP build 132, there are four tracks in this release. One is a track containing all mappings of reference SNPs to the human assembly, labeled "All SNPs (135)". The other three tracks are subsets of this track and show interesting and easily defined subsets of dbSNP:

Common SNPs (135): uniquely mapped variants that appear in at least 1% of the population Flagged SNPs (135): uniquely mapped variants, excluding Common SNPs, that have been flagged by dbSNP as "clinically associated" Mult. SNPs (135): variants that have been mapped to more than one genomic location By default, only the Common SNPs (135) are visible; other tracks must be made visible using the track controls.

You will find the four SNPs (135) tracks on the Human Feb. 2009 (GRCh37/hg19) browser in the "Variation and Repeats" group.

Many thanks to dbSNP at NCBI for the data, and to Mary-Claire King at the University of Washington for helpful comments that motivated us to enhance our dbSNP annotations. The tracks were produced at UCSC by Angie Hinrichs and Brooke Rhead.