Hi,
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
Best,
Geert
--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
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