where can I find the description of the columns for snp147.txt.gz in the UCSC website ??
List Of Dbsnp Rsids And Their Positions
Where can I get a list of the RSIDs and chromosome locations for a specific dbSNP build? Build 132 in my case
I've tried:
- the ftp download site (doesn't seem to be there)
- the Ensembl BioMart server (crashes due to out of memory error)
Thanks in advance!
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3 answers
From the UCSC download site:
curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz" |\
gunzip -c |\
cut -d ' ' -f 2,3,4,5
chr1 10326 10327 rs112750067
chr1 10433 10433 rs56289060
chr1 10439 10440 rs112155239
chr1 10439 10440 rs112766696
chr1 10468 10469 rs117577454
chr1 10491 10492 rs55998931
chr1 10518 10519 rs62636508
chr1 10532 10533 rs114315702
chr1 10582 10583 rs58108140
chr1 10827 10828 rs10218492
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http://genome.ucsc.edu/cgi-bin/hgTables setting the proper parameters and click "describe table schema"
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This link is broken- probably outdated. Does anybody have an updated link?
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You can get this in simple table format from UCSC. http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp132.txt.gz
Or from their mysql:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -NA \
-e "select chrom, chromStart, chromEnd, name from hg19.snp132" hg19 > snp132.hg19.txt
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This link is also broken. Is there an updated link?
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