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Old 04-30-2010, 06:15 AM   #1
dzmtnvmt
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Location: Shanghai China

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Default how to fetch the snp allele frequency?

hello,everyone~

I now need a txt file with several columns, which contains the rs ID of snp, frequency of each allele. I was told to download the SNPAlleleFreq.bcp file from ncbi. But i don't know exactly what each column tells about, and who to fetch the snp allel freq. So i need some help.

thanks very much
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Old 05-18-2010, 07:27 AM   #2
epigen
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Hi,

if you haven't found another way yet, I'd recommend downloading the snp130 table from the UCSC genome browser. I suppose you'd like to have SNPs for the latest human genome? Then go to http://hgdownload.cse.ucsc.edu/golde...hg19/database/
and download snp130.txt.gz

A description of the columns is available in the "Tables"
http://genome.ucsc.edu/cgi-bin/hgTables?command=start
when you select from the dropdown menu
group: Variations and Repeats track: SNPs (130)
table: "snp130"
and then hit "describe table schema"

Hope this helps
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Old 01-24-2011, 09:54 AM   #3
husamia
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I have the same question, I am interested in frequency information from dbsnp132. I have chromosomal positions and rs#s and want to get frequency information. My goal is to filter out common snps since 1000genomes data is supposed to discover rare variations <1%.
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Old 06-21-2011, 04:44 AM   #4
megnetz
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Hello! I checked one biallelic SNP in this database (snp131) to determine allele freq. I found an average heterozygosity of 0.5. I guess this is because there is no data on allele frequency? Or is it actually 0.5? In that case allele frequency should also be 0.5 according to hardy-weinberg?

Thanks for your help!
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