GA C1.4 1.4

What is the relationship between the PCT and the EPC? 
For international applications which are the subject of proceedings before the EPO in any of its functions (see point 1.1.004), the provisions of the PCT and its Regulations ("the PCT Rules") apply, supplemented by the provisions of the EPC.
In case of conflict between the provisions of the EPC and those of the PCT or the PCT Rules, the PCT prevails.
As from the entry into force of EPC 2000 on 13 December 2007 the EPO has withdrawn all notifications of incompatibility with PCT provisions.[ 11 ]
OJ 2007, 692
In accordance with the principle of the prevalence of the PCT, applicants should refer to the PCT International Search and Preliminary Examination Guidelines ("GL/ISPE", "ISPE Guidelines") for information on search and examination practice and procedure before the EPO as ISA, SISA and IPEA. In addition, they may also refer to the PCT-EPO Guidelines. In these procedures, the Guidelines for Examination in the European Patent Office (GL/EPO) apply only to the extent that they can be applied in conformity with the supplementary role of the EPC in the international phase (see point 1.4.001).
In a number of cases the ISPE Guidelines leave a choice between alternative options, from which each ISA/IPEA may select the most appropriate. The options are set out in appendices to the chapters of the ISPE Guidelines. The EPO will choose the option most in line with its own practice under the EPC. A list of policy options chosen by the EPO is provided in the Annex to this Guide (see also point 3.2.003).
Moreover, in an agreement between the EPO and the International Bureau of WIPO ("Agreement EPO-WIPO") concerning the functioning of the EPO as International Authority (ISA, SISA and IPEA) all particulars of the work of the EPO in that capacity are set out. The latest agreement of October 2017 entered into force on 1 January 2018. 
Official Notices (PCT Gazette) –28 March 2019 page 45 

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EPC Articles

EPO Guide for Applicants, part II Int.

EPO Guide for Applicants, part II Int. - C The EPO as ISA and SISA

Offical Journal of the EPO