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Old 02-02-2011, 09:35 AM   #1
Nataiki
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Location: Uruguay

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Default 1000 genomes

Hello everybody, Im new here... and would appreciate any help! Maybe its an obvious question but Im trying to find out how to interrogate the 1000 genomes project data base. I want to see if some SNP are present in the data from the project.
Is there any way to upload my snp and see wether if it was found on the 1000 genomes?
Thanks very much!
Natalia
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Old 02-03-2011, 12:20 AM   #2
ulz_peter
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You could try that:

http://medgen.ua.ac.be/~gvandeweyer/index.php?page=1000
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Old 02-03-2011, 01:56 AM   #3
doc.ramses
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I like the ANNOVAR tool:

http://www.openbioinformatics.org/annovar/
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Old 02-03-2011, 01:58 AM   #4
laura
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The variant calls from the 1000genomes project come in VCF format which is describes here http://vcftools.sourceforge.net/specs.html

If you can put your own snps into vcf format you would be able to use a tool like http://vcftools.sourceforge.net/perl...ml#compare-vcf to compare your set to the 1000genomes set.

If you are interested in subsets of 1000 genomes data as the whole file is quite large you can use a program called tabix to get subsections of the file

tabix comes from here
http://sourceforge.net/projects/samtools/files/tabix/

and a command line like

tabix -h ftp://ftp.1000genomes.ebi.ac.uk/vol1...notypes.vcf.gz 1:1-1000000

would get you all the variants in the first megabase of chr1.
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Old 02-04-2011, 04:42 AM   #5
Nataiki
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Thanks very much everybody for such a quickly reply!!!!
Saludos
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