The Annotation File (Required for Association Tests)

Gene-based association tests are performed using FBAT and OVPDT. Therefore, an annotation file is required to define gene regions. Moreover, IBD sharing statistics and disease model status will be added to the annotation file if the file is provided. The file must have at least four essential columns, starting with the column names "chromosome position referenceBase geneList"

For example, in annotation.txt:

chromosome position referenceBase geneList
1 7324503 A CAMTA1
1 7324547 T CAMTA1
1 7324959 T CAMTA1
1 7326621 G CAMTA1
1 7326747 A CAMTA1
1 7331060 C CAMTA1

Extra columns can be added in the file. The annotation file should be based on NCBI 37/hg19. The annotation file can be generated using SeattleSeq (http://snp.gs.washington.edu/SeattleSeqAnnotation138/).
Command line options:
--Anno_file filename
Example:
--Anno_file annotation.txt