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Old 02-20-2012, 05:37 AM   #1
Location: Milano, Italy

Join Date: Aug 2011
Posts: 93
Default IGV-dbSNP

Dear all,
I would like to load in IGV last release of human dbSNP, where can I download it?
paolo.kunder is offline   Reply With Quote
Old 02-20-2012, 02:18 PM   #2
Senior Member
Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

Download the latest dbSNP vcf file from NCBI ftp site. Use IGVtools to index, not actually sure you need to, then load the vcf just like you do a bam file
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Old 02-21-2012, 12:15 AM   #3
Jim Robinson
Location: Boston, MA

Join Date: May 2009
Posts: 75

Actually if you download the gzipped (tabix) file and the index (...gz.tbi) you don't need to do anything, just load it. I'm assuming these files are tabix-indexed.

Also, you can actually load it directly by ftp by copy & pasting the URL to "Load from URL" (assuming its tabix indexed, i.e. it has a "tbi" file). Performance will be better if you download it though.

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