META_DATA_FILEMandatory. The path to the metadata file (see below). Can be a path relative to the
gwasfolder next to the parameters file or an absolute file.
DATA_LOCATIONDefault: parent directory of the metadata file. The directory that functions as the path against which the data files referenced in the metadata file are to be found.
HG_VERSIONDefault: 19. Either 18 or 19. The reference assembly to use.
A TSV that functions as an index for several analyses in the same study. This pipeline uses the following mandatory columns:
STUDYMandatory. The name of the study (max: 50 characters).
DATA_TYPEMandatory. Must be
ANALYSIS_NAMEMandatory. A short name for the analysis. It should not include the string
"test"(or any variant where one or more of the characters are uppercase), otherwise the analysis will not show up in GWAVA. Max: 500 characters. The tuple
(STUDY, ANALYSIS_NAME)must be unique.
INPUT_FILE. Mandatory. The name of the file containing the analysis' data.
Other columns can provide more meta data about the analysis. The full list can be seen by looking at the example file.
An example analysis data file can be found here. No column is mandatory, except for
RS_ID. However, the
P_VALUE should also be given for most functionality to work. Alleles may contain only one character.