Variant Sites In The Human Genome

Question

[win]

hi all, i wanted to query for all sites in the human genome where variants occur. for e.g if we use dbSNP in vcf format one can run a bedIntersect on that.

is there any such file for the entire human genome?

thanks, ashwin

[Alex Paciorkowski]

The file for all sites in the human genome where variants occur = the entire human genome. If you are asking where common variants occur, that is a different story. dbSNP is a good start. If you want to add in rare variants, you can use the data from 1000genomes, and add in exome data from the Exome Variant Server. Then you have the whole issue of structural variation, copy number variants (common around segmental dups and other rare sites). Some of that can be found in the Database of Genomic Variants. But really any site in the genome can be a point of variation. Some sites more so than others.

Answer 1

[JC]

maybe you can use Kaviar: http://db.systemsbiology.net/kaviar/