Common Input Options¶

--region: input multi region list (comma delimited) - “--region 22:17257787-19792353,X,Y”. Or input a region file - “--region /nfs/goldstein/software/atav_home/data/region/example.txt”

--out: input output directory path. - “--out /myworkspace/atav_output”

Category Specific Command Options¶

• Variant Level Filter Options
• Annotation Level Filter Options
• Genotype Level Filter Options
• Cohort Level Filter Options

Note:
All Genotype Analysis Functions support filters from all categories.
All Variant Annotation Functions support filters for Variant and Annotation categories.
All Coverage Analysis Functions and External datasets functions do NOT support above filters.
Most functions have their own sub options.