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• Installation and script setup

  No due date

  •0/4 issues closed
  0% complete4 open0 closed

• Visual validation assistant

  Add a script that will generate screenshots of the variants' alignment, for example in the IGV browser, for validation. This should be done for all variants that pass filtering. At least one control should be visible in the screenshot. The script should be able to run for a single variant or a list of variants, and it should generate a folder containing the screenshots. The script should be able to run on a server without a graphical user interface. Control samples should be able to be added to the screenshots. Ideally, the read layout (e.g., pairs, sorting, soft clipping, etc.) and screenshot size can be configured.

  No due date

  •0/2 issues closed
  0% complete2 open0 closed

• Phenotype filtering functionallity

  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.

  No due date

  •4/8 issues closed
  50% complete4 open4 closed