SNP discovery data release policy
Following quality control review, raw data from sequencing and SNP identification is transferred from the
sequencing facility in Tucson to the Bioinformatics group in Boston, where it is processed through the PhAT
Bioinformatics pipeline and published in detail on the private website for review by all PhAT investigators.
The reference sequence, raw genotype data for each subject sequenced and SNP flanking sequences, sample specific
tables of allele and genotype frequencies and counts are prepared and published for review within a few hours of
transfer of the raw data from the Sequencing facility. Haplotype inference and pairwise LD estimation involve
substantial computing time and may take several days to complete. These are published for review as soon as they
Within one week of internal review release, all material is made available on the public website
To ensure that visitors can quickly locate newly published material, the public site home page is automatically
updated to show all SNP released within the previous 30 days. A wide range of prepared reports are available for
all published SNP, but in order to ensure that visitors can obtain SNP data in formats which suit their individual
needs, we make a dynamic web application available which permits site visitors to
tailor their own reports. Visitors may choose a variety of report
formats and may limit the output to one or more samples and exclude SNP below arbitrary minimum allele frequencies.
Like the prepared reports, outputs from these visitor-specified reports may be viewed as web pages or downloaded
as text or spreadsheet files.
Software to prepare material for submission of SNP discoveries to dbSNP is nearing completion. SNP discoveries
will be submitted to dbSNP as soon as practicable.