Setting Treatment Options and Practices for Veteran Suicide and Substance Abuse Act or the STOP Veteran Suicide and Substance Abuse Act This bill requires the Department of Veterans Affairs (VA) to complete the development of clinical practice guidelines for the treatment of post-traumatic stress disorder (PTSD), military sexual trauma, and traumatic brain injury that is occurring simultaneously with substance use disorder or chronic pain. The VA, the Department of Defense (DOD), and the Department of Health and Human Services must create a Trauma and Comorbid Substance Use Disorder or Chronic Pain Work Group to develop such clinical practice guidelines in consultation with other work groups, including the Substance Use Work Group. The bill also requires the VA and DOD (through the Assessment and Management of Patients at Risk for Suicide Work Group) to issue an update to the VA/DOD Clinical Practice Guideline for Assessment and Management of Patients at Risk for Suicide that considers gender- and age-specific factors.