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BamExtract tool help

BamExtract (2024_08-113-g94a3b440)

Extract reads from BAM/CRAM by read name.

Mandatory parameters:
  -in <file>        Input BAM/CRAM file.
  -ids <file>       Input text file containing read names (one per line).
  -out <file>       Output BAM/CRAM file with matching reads.

Optional parameters:
  -out2 <file>      Output BAM/CRAM file with not matching reads.
                    Default value: ''
  -ref <file>       Reference genome for CRAM support (mandatory if CRAM is used).
                    Default value: ''

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).

BamExtract changelog

BamExtract 2024_08-113-g94a3b440

2023-11-30 Initial implementation.

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