VCF data

First create dump to be sure:

sudo -u postgres LANG=en_US pg_dump transmart > transmart_<version>.sql
(Use locale -a to check which locales you have)

delete from deapp.de_variant_subject_detail where dataset_id='TCGAOV';
delete from deapp.de_variant_subject_summary where dataset_id='TCGAOV';
delete from deapp.de_variant_subject_idx where dataset_id='TCGAOV';
delete from deapp.de_variant_population_data where dataset_id='TCGAOV';
delete from deapp.de_variant_population_info where dataset_id='TCGAOV';
delete from deapp.de_variant_metadata where dataset_id='TCGAOV';
delete from deapp.de_variant_dataset where dataset_id='TCGAOV';
delete from deapp.de_subject_sample_mapping where trial_name='TCGAOV' and platform='VCF';

delete from deapp.de_gpl_info where platform = 'VCF_hg36';

Please note that the SQL queries mentioned there only delete the VCF data and not the i2b2 concept and observations related to the VCF data. These can be removed using the i2b2_backout_trial procedure (with all clinical data) or manually. These i2b2 tables to check for the vcf nodes are: i2b2metadata.i2b2, i2b2metadata.i2b2_secure, i2b2demodata.concept_dimension. For example:

delete from I2B2METADATA.I2B2 where c_fullname = '\Private Studies\TCGAOV\DNASeq\';
delete from I2B2METADATA.I2B2_SECURE where c_fullname = '\Private Studies\TCGAOV\DNASeq\';
delete from I2B2DEMODATA.CONCEPT_DIMENSION where concept_path = '\Private Studies\TCGAOV\DNASeq\';

References

1. Original text https://wiki.transmartfoundation.org/display/transmartwiki/TranSMART+Guide+for+Manual+Data+Deleting