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Overview Advances in high-throughput sequencing, genotyping, and characterization of haplotype diversity are consistently generating vast amounts of genomic data. Single Nucleotide Polymorphisms (SNPs) are the most common type of genetic variation [1]. In the recent years the number of known SNPs has been increasing exponentially [2]; the last release of the NCBI’s dbSNP database [3] contained more than 55 million human SNPs. SNPs are interesting as both markers of evolutionary history and in the context of their phenotypic manifestations (e.g. characteristic traits and diseases). However, due to their sheer number, detailed experimental annotations are impossible and computational inference is severely limited by the required resources. SNPs also present a challenge for visualization and storage. In line with the increasing interest in the genetic variation analysis and annotation, on July 14th, 2012 [4] we organized the second SNP Special Interesting Group (SNP-SIG) meeting at the ISMB’12 in Long Beach, CA. This meeting attempted to summarize the field’s research advances in the directions of “Annotation and prediction of structural/functional impacts of coding SNPs” and “SNPs and Personal Genomics: GWAS, populations and phylogenetic analysis”. The discrepancy between the significant availability of the SNP data and the current lack of its interpretation requires the development of new computational annotation methods. The analysis of genetic variation is a key factor for the understanding of the genomic information. The SNP-SIG provides a forum necessary for the organization of a research network facilitating the exchange of ideas and for the establishment of new

Thoughts from SNP-SIG 2012: future challenges in the annotation of genetic variations