2.216: Fighting is enjoined on you, and is an object of dislike to you; and it may be that you dislike a thing while it is good for you, and it may be that you love a thing while it is evil for you, and Allah knows, while you do not know.
5.33: The punishment of those who wage war against Allah and His apostle and strive to make mischief in the land is only this, that they should be murdered or crucified or their hands and their feet should be cut off on opposite sides or they should be imprisoned; this shall be as a disgrace for them in this world, and in the hereafter they shall have a grievous chastisement,
8.12-13: When your Lord revealed to the angels: I am with you, therefore make firm those who believe. I will cast terror into the hearts of those who disbelieve. Therefore strike off their heads and strike off every fingertip of them. This is because they acted adversely to Allah and His Apostle; and whoever acts adversely to Allah and His Apostle -- then surely Allah is severe in requiting (evil).
9.29: Fight those who do not believe in Allah, nor in the latter day, nor do they prohibit what Allah and His Apostle have prohibited, nor follow the religion of truth, out of those who have been given the Book [Jews and Christians], until they pay the tax in acknowledgment of superiority and they are in a state of subjection.
(Emphasis added—probably unnecessarily)
You can see if these are taken out of context by reading more with this online Koran.
Note there is no analogy between these verses and the difficult passages in the Old Testament, such as in Joshua, where entire cities are laid to waste at God's command. Those were specific this-place this-time one time only commands that, while they hard for us to understand, are far different from the open-ended license to kill and mutilate found in the Koran.