GenesToTranscripts.md

GenesToTranscripts tool help

GenesToTranscripts (2025_03-90-gd5865e32)

Converts a text file with gene names to a TSV file with these columns: gene name, transcript name, biotype, exon count, flags

Best transcript is determined according this order: 'preferred transcript in NGSD', 'MANE select', 'Ensembl canonical', 'longest coding transcript', 'longest transcript'
Relevant transcripts are: 'preferred transcript in NGSD', 'MANE select', 'MANE plus clinical', 'Ensembl canonical' (if none of those exist, the longest coding or longest transcript is used)

Mandatory parameters:
  -mode <enum>      Mode: all = all transcripts, best = best transcript, relevant = all relevant transcripts, mane_select = only MANE select transcripts.
                    Valid: 'all,best,relevant,mane_select'

Optional parameters:
  -in <file>        Input TXT file with one gene symbol per line. If unset, reads from STDIN.
                    Default value: ''
  -version          Append transcript version to transcript name.
                    Default value: 'false'
  -out <file>       Output TSV file. If unset, writes to STDOUT.
                    Default value: ''
  -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).

GenesToTranscripts changelog

GenesToTranscripts 2025_03-90-gd5865e32

2025-05-26 Added columns and reordered columns.
2023-05-26 First version.

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