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cancerit / cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel
http://cancerit.github.io/cgpPindel/
GNU Affero General Public License v3.0
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Calling InDel with only tumor sample #54

Closed tenglaowu closed 7 years ago

tenglaowu commented 7 years ago

Dir sir, Is there any possible to call somatic InDel without Normal sample but only tumor sample?

keiranmraine commented 7 years ago

As per the email conversation we had:

cgpPindel is only designed to run with a single tumour and a matched normal. However, you can run without a real matched normal dataset by creating an empty one for the '-normal' parameter.

A method to create the required files for a 'null' normal is described in the cgpPindel protocol paper under the 'pindel_np.gff3.gz' section of 'Support Protocol 2: Static Reference Files'. You should use steps 1-3 to generate the empty dataset and then run analysis as normal.