zCall/InstructionsForGeneratingGSreport.txt at master · jigold/zCall · GitHub

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zCall: A Rare Variant Caller for Array-Based Genotyping
(GenomeStudio Report Version - without the use of an EGT file)

Author: Jackie Goldstein - jigold@broadinstitute.org
Contact: Benjamin Neale - bneale@broadinstitute.org
May 8th, 2012

***The Illumina provided Code was provided as-is and with no warranty as to performance and no warranty against it infringing any other party's intellectual property rights.
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Directions for Generating GenomeStudio Report Input to zCall:

In GenomeStudio select 'Full Data Table' tab.
Click on 'Column Chooser' icon.
In Displayed Columns select 'Name', 'Chr','Position', and all your samples.
In Displayed Subcolumns select 'GType', 'X' and 'Y'.
Hit OK then click on 'Export displayed data to a file' icon.