Association test

Two family-based association tests can be performed in FamPipe. If imputations were performed, FamPipe will use the ped file with the imputed data to run the association tests.

Command line options:
  • Running OVPDT. OVPDT is a SKAT-type family-based association test for rare variants.
    --Association 1
  • Running FBAT. FBAT is a burden-type family-based association test for rare variants.
    --Association 2
Related options:
  • An annotation file is required to run the association test.
    --Anno_file filename
    Example:
    --Anno_file annotation.txt
  • Association in the presence of linkage. By default, association tests will be performed for all genes provided in the annotation file. Alternatively, association tests can be performed in linkage regions to save running time. This is particularly useful when imputation is performed in linkage regions and association tests are performed based on the imputed data. This option should be used with --Linkage.
    --APL
Association test Output:
For example:
Association_chr1.txt
Gene #_of_SNPs p_value
TBX15 354 0.551

There are three columns in the association test result file. The first column is the name of genes, the second column is the number of snps in genes and the third columns is the association p_value.

Error/Warning:
  • Error : could not find '--Anno_file'.
    If you see this message, please add "--Anno_file" option in your command and provide annotation file as well.
  • Error : could not open "Annotation_chrX.txt" file.
    If you see this message, please check your Annotation_chrX.txt file whether is in the folder that you assign in command.