Was it a civil war?

Hello Rabbi, In the Book of Judges, it is mentioned that the tribe of Ephraim complained against Jephthah the Gileadite and wanted to burn his house. Jephthah and the Gileadites killed forty-two thousand from the tribe of Ephraim. Was this a civil war? Are there any commentaries regarding whether there was a justification for killing on such a scale?

Hello and happy holiday 

Jephthah's justification for killing the people of Ephraim was the fact that they came to kill him. 

Additionally, in Radak's commentary, it is mentioned that their killing was due to their sins. 

Nevertheless, it is stated in Midrash Tanchuma that Jephthah was held accountable for their killing, and because of this act, it was decreed that his daughter would die. 

Radak, Judges, Chapter 12
And this great killing was a punishment for the sins that were hidden in the tribe of Ephraim:

Midrash Tanchuma (Warsaw), Parashat Bechukotai, Sign 5
And they did not find a way for Jephthah to annul his vow because of those he slaughtered from the tribe of Ephraim, and it is said about him (Proverbs 28) "A poor man who oppresses the poor is Jephthah, who was poor in Torah like the trunk of a sycamore, who oppressed the poor, as it is said (Judges 12) 'and they said to him: say 'Shibboleth', and he said 'Sibboleth', and he could not pronounce it correctly, and he slaughtered them, therefore a sweeping rain and no bread, he had someone who could annul his vow, but no bread, because the Holy One, blessed be He, hid the law from them so they would not find a way to annul his vow, he rose and slaughtered them,