Tuesday, November 30, 2010

dbSNP file naming convention

>ls ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606

dr-xr-xr-x 2 ftp anonymous 4096 Feb 28 2010 1000Genomes
dr-xr-xr-x 2 ftp anonymous 4096 Nov 15 14:52 ASN1_bin
dr-xr-xr-x 2 ftp anonymous 4096 Nov 15 14:55 ASN1_flat
dr-xr-xr-x 2 ftp anonymous 4096 Nov 29 16:39 ASN1_flat_b131
dr-xr-xr-x 3 ftp anonymous 4096 Feb 28 2010 GWAS_arrays
lr--r--r-- 1 ftp anonymous 17 Oct 28 20:17 README_human_9606_B132.txt -> /snp/00readme.txt
dr-xr-xr-x 3 ftp anonymous 4096 Sep 30 18:55 VCF
dr-xr-xr-x 2 ftp anonymous 4096 Nov 15 15:07 XML
dr-xr-xr-x 2 ftp anonymous 4096 Nov 15 15:08 chr_rpts
dr-xr-xr-x 7 ftp anonymous 4096 Sep 28 20:29 database
dr-xr-xr-x 2 ftp anonymous 167936 Nov 3 15:33 gene_report
dr-xr-xr-x 2 ftp anonymous 4096 Feb 28 2010 genome_report
dr-xr-xr-x 3 ftp anonymous 4096 Oct 14 17:39 genotype
dr-xr-xr-x 27 ftp anonymous 4096 Oct 14 18:20 genotype_by_gene
dr-xr-xr-x 3 ftp anonymous 4096 Feb 28 2010 haplotypes
dr-xr-xr-x 5 ftp anonymous 4096 Nov 15 19:05 misc
dr-xr-xr-x 2 ftp anonymous 4096 Nov 15 15:14 rs_fasta
dr-xr-xr-x 15 ftp anonymous 4096 Apr 5 2010 ss_fasta
dr-xr-xr-x 2 ftp anonymous 45056 Nov 17 21:14 viewBatch

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example:
14-12162-MKK.vcf.gz
14 -> Chromosome 14
12162 -> dbSNP population ID (http://www.ncbi.nlm.nih.gov/projects/SNP/snp_viewTable.cgi?pop=12162)
MKK -> Three letter population identifier (http://ccr.coriell.org/sections/collections/NHGRI/?SsId=11)

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