A pipeline for running Zcall and Opticall on Illumina Exome Chip Datasets. This workflow will handle all the file parsing and run both callers and compare the output bed files.

Repository: https://github.com/KHP-Informatics/chip_gt

Author: Amos Folarin
Organisation: KCL/SLaM
Email: amosfolarin@gmail.com


1) Sun Grid Engine
2) Zcall
3) Opticall


1) Read notes (GenomeStudio.SOP.v1.2.docx – the most up-to-date SOP are on the confluence page http://confluence.brc.iop.kcl.ac.uk:8090/display/PUB/Production+Version%3A+Illumina+Exome+Chip+SOP+v1.4 ) on processing the data in GenomeStudio
2) Generate the GenomeStudio Report file (as required for by Zcall, parses this as input for both Zcall and Opticall rare callers):

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

3) Copy the template.workflow.sh into a working directory
4) Edit the paths as indicated in this script for your installations of Zcall and Opticall etc.
5) Specify the datapath and basename variables for the GenomeStudio Report generated in step (2)
6) Execute the pipeline bash script (template.workflow.sh).

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