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BedpeGeneAnnotation.md

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BedpeGeneAnnotation tool help

BedpeGeneAnnotation (2024_08-110-g317f43b9)

Annotates a BEDPE file with gene information from the NGSD.

Mandatory parameters:
  -in <file>              Input BEDPE file containing the SVs.
  -out <file>             Output BEDPE file containing the annotated SVs.

Optional parameters:
  -add_simple_gene_names  Adds an additional column containing only the list of gene names.
                          Default value: 'false'
  -test                   Uses the test database instead of on the production database.
                          Default value: 'false'

Special parameters:
  --help                  Shows this help and exits.
  --version               Prints version and exits.
  --changelog             Prints changeloge and exits.
  --tdx                   Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
  --settings [file]       Settings override file (no other settings files are used).

BedpeGeneAnnotation changelog

BedpeGeneAnnotation 2024_08-110-g317f43b9

2023-05-10 Added column with gene names at breakpoints.
2020-01-27 Bugfix: 0-based BEDPE positions are now converted into 1-based BED positions.
2020-01-21 Added ability to reannotate BEDPE files by overwriting old annotation.
2020-01-20 Updated overlap method, refactored code.
2020-01-14 Added handling of duplicates.
2020-01-08 Initial version of this tool.

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