molgenis/molgenis-pipelines — pull request #145 by kantale (2014-06-20 16:24:05+00:00)
Title: fixed paste tab problem

Copying from Patrick/Freerk mail:
Hi Freerk and Alex,

There is a small bug in the imputation script. Gen files can only contain spaces but contain a tab after the alleles

--- 1-10478 10478 C G 1 0 0
Alex:
This is indeed a serious bug:
http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html#Genotype_File_Format
although it does not make clear what is the proper delimiter for .gen files, it does make it clear for .sample files:
Use spaces to separate the entries of the sample file and not TABS.

Fix: I added the -d ' ' parameter in paste command