Resource 1817

Name: SNP posterior data

The snp-posterior data are the parameters for the posteriors from the Affymetrix calling algorithm which can be used for determining the cluster ellipses in cluster plots or re-estimating the genotype probabilities. This file is a linux tar containing multiple files as detailed below. To extract use the command

tar -xvf

The snp-posterior data are in .bin files, which are simple binary files. There are 33 parameters per SNP per batch (3,498 per SNP). Each parameter is represented by a 4-byte float. The set of values for each SNP are ordered consecutively by batch (as given in the batch file). This is analagous to a matrix with rows=SNPs and columns=batch_parameters. There are 7 parameters for each genotype cluster BB, AB,AA and a fourth set of 12 parameters (CV) from Affymetrix's algorithm. The only missing values are for SNPs which only appear on one array or the other but not both, the missing value is the standard binary NaN because the range of allowed values includes both 0 and negative numbers.

There is one BIM file per chromosome listing the order of the SNPs (see Resource 1963). These have the same order as for the calls data except for chrX, see below).

Affymetrix call diploid (chr1-22, XY SNPs) and haploid (chrY, chrMT SNPs) SNPs differently. On chrX females are diploid and males are haploid giving two sets of parameters per SNP per batch. In the .bin snp-posterior chrX file, for each SNP the diploid and then the haploid snp-posteriors are given consecutively. The order of the SNPs is given in the BIM files, the haploid SNPs on chrX are appended with ":1" following Affymetrix notation. The snp-posterior BIM files for chr1-22,Y,XY,MT are the same as the calls, but the chrX snp-posterior BIM file has twice as many lines.

A single .batch file the order of the batches in the binary file. This is identical for all chromosomes.

An additional file has been supplied containing the MD5 values of the datafiles.

This resource be downloaded or viewed using the link: ukb_snp_posterior.tar