Command 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”

Variant Level Filter Options

Annotation Level Filter Options

Genotype Level Filter Options

All Genotype Analysis Functions support all above filter options.
All Variant Annotation Functions support Variant and Annotation Level filter options.
All Coverage Analysis Functions and External datasets functions does NOT support above options.
Most functions have their own sub options.