There is a missing parameter in the unified genotyer config from the iuc gatk2 wrapper: The following line should be added around line 204 (just before </expand></inputs>):

<param name="sample_ploidy" type="integer" value="2" label="Sample Ploidy (number of allles). For tumour, set to 2x the number of expected subclones" help="-ploidy,--sample_ploidy" />

Without this line, activating the advanced analysis options causes the job preparation to fail because there is a reference to it in the <command> section

gatk2 wrapper used:
version : 8bcc13094767
hg tip:
changeset:   3:2553f84b8174
tag:         tip
user:        iuc
date:        Wed Feb 19 04:39:38 2014 -0500
summary:     Uploaded




Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be

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