wtsi-npg/genotyping — pull request #231 by iainrb (2014-03-14 10:32:03+00:00)
Title: Changes to identity metric

* See RT ticket #379709
* Compare Sequenom plex file with Plink SNP list and find shared SNPs. If shared SNPs are too few, omit the identity check for *all* samples. (Default is 8 SNPs required for identity check.) Otherwise, compute identity on shared Plink/Sequenom calls and evaluate against threshold.
* Output identity results in JSON format
* Updated documentation, reports and tests
* Refactored comparison of failed samples for greater clarity. Also moved most identity check code from command-line script to the new Identity.pm module.