A crane attached to a barge pulled the boat from the Lake on Monday, where it had been submerged in 80 feet of water.
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Divers attached a sling to the 33-foot, 4-ton vessel, then raised and drained it, officials said. It was to be loaded onto a vehicle and turned over to the National Transportation Safety Board.
Coast Guard Lt. Tasha Sadowicz of the agency's St. Louis office said the boat that capsized and sank was known as "Stretch Duck 07." Like all 22 duck boats in operation in Branson, it was required to undergo annual inspections. The most recent was in February.
But Sadowicz said the Coast Guard's "certificate of inspection" placed limits on when the boats can enter the water based on wind speed and "sea state," which refers to the height of waves.
Sadowicz did not have information on Stretch Duck 07's limits but said they will be a focal point of the investigation.
Some witnesses have said the lake was calm and the storm came up suddenly Thursday evening. Sadowicz said investigators want to find out if operators were adequately monitoring the weather and should have reasonably known a storm was approaching.
At a news conference in Branson on Monday, Coast Guard Capt. Scott Stoermer said the investigation will also look into whether the boat captain followed company guidelines regarding use of life jackets.
Missouri law requires boat passengers ages 7 and younger to wear life jackets, but commercial vessels like the duck boats are exempt. The law requires enough life jackets for passengers and crew, and jackets that fit all of the children. Whether to advise passengers to use life jackets is an "operation decision" made by the captain, Stoermer said.
Several survivors made it to safety by climbing aboard another sightseeing boat that was nearby.
Many survivors told Missouri State Highway Patrol chaplain Steve Martin that they were able to swim to the Branson Belle paddle-wheeler. Some climbed up the paddle wheel itself. Others clung to the side of the boat until bystanders pulled them to safety.
"The waves were kind of pushing them toward the boat," Martin said.