A 9-year-old boy, 5-year-old boy and 3-year-old boy were among those that were killed.
The three-year-old son, man and woman had died at the scene of the horrific shooting, while the five and nine-year-old children died in hospital.
An 11-year-old is in surgery after being wounded in the shooting.
Prior to the incident, reports said an identified person called police from the home around 6a.m., but remained silent on the phone. As they travelled there another call came from a neighbour saying they heard a sound coming from the home that sounded like a nail gun.
Officers received no answer when they knocked on the front door of the granny flat, so they walked around back and through a window could see a child on the ground covered in blood, Dobbs said. They broke through the window and found "several people down" suffering from apparent gunshot wounds, Dobbs said. Three others were rushed to an area hospital, where a 5-year-old boy and a 9-year-old boy were also pronounced dead.
Dobbs said the mother and four children lived in the granny flat adjacent to the main house, where other family members lived.
"I just pray for that family", one neighbor said. At that time, police gave the wife with information as to how to retain a restraining order against her husband.
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The shooting happened in Flintridge Drive in the Paradise Hills neighborhood of San Diego on Saturday morning.
Neighbours told the San Diego Union-Tribune they often saw the boys outside playing with their dog or riding their bicycles.
"The man was trying to get some tools from his wife while they were separated".
Dobbs said the crime scene was so gruesome it traumatized even the arriving officers, who carried the children out of the house in a desperate effort to save them. The suspected shooter is among those killed and the sole survivor, an 11-year-old boy, remains in "very critical" condition.
"It appears to be a tragic case of domestic violence-murder suicide", San Diego Police Department homicide Lt. Matt Dobbs told reporters Saturday afternoon.
Saturday wasn't the first time authorities responded to the home.
The names of the victims have not been released.