Urine, human and animal faeces, garbage and rotten food littered the floor, police said, and heaps of debris blocked off parts of the house.
The allegations came from extensive interviews with numerous children, who range in age from 12 years to 4 months.
Authorities allege Rogers put the children in a situation that was likely to great bodily injury or death.
Allen was arrested Friday and pleaded not guilty to nine counts of felony torture and six counts of felony child abuse. Solano County prosecutors included the horrific details in a motion to increase the bail for Rogers, who was charged with nine counts of felony child abuse.
The matter unfolded March 31 when the oldest child, a 12-year-old boy described as developmentally delayed with the capacity of an 8-year-old, disappeared from his house in the 2000 block of Fieldstone Court.
At the Monday press conference, Solano County Chief Deputy District Attorney Sharon Henry said she was "horrified" by the statements made by several of the victims and that "as a parent, first and foremost in my heart ... we believe these children deserve justice". She declined to elaborate. Police removed the children and arrested Rogers on suspicion of neglect.More news: May 21: Virginia Voter Registration Deadline
Despite the gruesome charges against Allen, Rogers continues to stand by her man.
Ina Rogers, who has since been released, told reporters on Monday: "Anyone just needs to look into it and take my kids to the doctor alone, and all of these torture allegations will fall away, because there's no broken bones, no major scars - no nothing".
"I've been doing this a long time, I was a prosecutor for 22 years, and have not seen a case of such overwhelming evidence of mental, emotional, physical abuse by the hands of their parents", Solano County District Attorney Krishna Abrams said.
Police also said the children have burns, puncture wounds, and bruises - injuries consistent with being shot with a pellet or BB gun. The other rooms were used as a master bedroom, playroom and meditation room.
In this photo provided by the Daily Republic, Ina Rogers, center, appears in Solano County Superior Court in Fairfield, Calif., Wednesday, May 16, 2018, to face multiple charges of felony child abuse.
Allen said his children had no marks of abuse when they were taken by Solano County Child Welfare Services on March 31. Prosecutors said at a Monday press conference they were in the process of determining whether additional charges would be filed against Rogers.More news: Rui Faria could be offered a huge job after leaving Manchester United
Rogers said she homeschooled the children, but there is no record she registered with the state as required by law. She did not say why. But absolutely not, my husband is an unbelievable person.
"On a continuous basis the children were getting punched, strangled, bitten, shot with weapons such as crossbows and bb guns, hit with weapons such as sticks and bats, subjected to "waterboarding" and having scalding water poured on them", Juarez wrote.
Rogers said she felt unfairly judged for her lifestyle.
She is estranged from her son and he has kept his family away from the children, she said.
Rogers says she home-schooled the children, but the two-story Fairfield, California, home was not registered as a private school and neither were three prior addresses where the family lived in Fairfield and Vallejo, according to the California Department of Education.
Allen denied being a Satanist in a jailhouse interview with local news station KCRA. "But I don't know how you can keep it quiet when you have 10 kids".More news: Mike Budenholzer hired as new head coach of Milwaukee Bucks