dnil / stranger

Tool to annotate outfiles from ExpansionHunter with the pathologic implications of the repeat

Stranger

Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.

Installation

git clone github.com/moonso/stranger
cd stranger
pip install --editable .

Usage

stranger --help
Usage: stranger [OPTIONS] VCF

  Annotate str variants with str status

Options:
  -f, --repeats-file PATH         Path to a file with repeat definitions. See
                                  README for explanation  [default: /Users/man
                                  smagnusson/Projects/stranger/stranger/resour
                                  ces/repeatexpansionsloci.tsv]
  --version
  --loglevel [DEBUG|INFO|WARNING|ERROR|CRITICAL]
                                  Set the level of log output.  [default:
                                  INFO]
  --help                          Show this message and exit.