The pipeline should be improved so that it can filter a delimited file containing phenotype information using the sample identifiers from the filtered variants.
The delimited file should have a long structure, with one row for each sample and one phenotype combination.
Depending on the output format, the phenotype information can be added to the output file or saved in a separate file.
This will necessitate the use of an additional script called "filter_phenotypes.sh."
It will be necessary to add parameters and options to the main "filter_variants.sh" script in order to control the phenotype filtering process.
The user is responsible for creating the phenotype file. It can be either a CSV or a TSV file.
This milestone will also necessitate the addition of a new section to the documentation that describes the phenotype file format as well as the new parameters and options.