Overridde the Doctrine UpdateSchemaCommand (doctrine:schema:update command).

CustomUpdateSchemaCommand.php

// src/AppBundle/Command/CustomUpdateSchemaCommand.php
<?php

namespace AppBundle\Command;

use Doctrine\Bundle\DoctrineBundle\Command\Proxy\UpdateSchemaDoctrineCommand;
use Doctrine\ORM\EntityManagerInterface;
use Symfony\Component\Console\Input\ArrayInput;
use Symfony\Component\Console\Input\InputInterface;
use Symfony\Component\Console\Output\OutputInterface;
use Symfony\Component\Console\Command\Command;

class CustomUpdateSchemaCommand extends UpdateSchemaDoctrineCommand
{
    /** @var EntityManagerInterface */
    private $em;

    /**
     * @param EntityManagerInterface $em
     */
    public function __construct(EntityManagerInterface $em)
    {
        $this->em = $em;

        parent::__construct();
    }

    /**
     * {@inheritDoc}
     */
    protected function configure()
    {
        parent::configure();
    }

    /**
     * {@inheritDoc}
     */
    protected function execute(InputInterface $input, OutputInterface $output)
    {
        $output->writeln('Hello world');
        $repository = $this->em->getRepository('AppBundle:Foo');

        // Perform your custom query

        return parent::execute($input, $output);
    }
}

services.yml

services:
    app.command.custom_schema_update_command:
        class: App\SportBundle\Command\CustomUpdateSchemaCommand
        arguments: ["@doctrine.orm.entity_manager"]
        tags:
            -  { name: console.command }

Related http://stackoverflow.com/a/36655069/4363634