Fixed bugs in supplied gender reporting and duplicate processing

wtsi-npg / genotyping

Components of the WTSI genotype analysis pipeline.

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Closed iainrb closed 8 years ago

iainrb commented 8 years ago

Fixes two minor bugs:

If no threshold is supplied for the duplicate metric (eg. for the Illuminus prefilter using call rate only), do not carry out preprocessing of the duplicate results
Correctly handle arbitrary codes for supplied gender (eg. -9) used in PLINK data