= Compare Sequence Data With Genotype Chip = Status: Alpha Authors: Patrick Deelen, Morris Swertz Tool to compare sequence data with data from genotyping chips. == Features == * Overview of concordance per sample * Matrix of all sequence samples vs all genotype samples * This is used to detected sample mix-ups * Performance per SNP == Input == The genotype data input is currently PED/MAP as generated by [http://pngu.mgh.harvard.edu/~purcell/plink/ plink]. Both QCed as non QCed data is supported. The following sequence file formates are supported * VCF * Q20 (as provided by BGI) * CNS == Future == * Plots to give more insight in SNP performance