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VcfAnnotateFromBed tool help

VcfAnnotateFromBed (2021_06-89-gbbd16264)

Annotates the INFO column of a VCF with data from a BED file.

Characters which are not allowed in the INFO column based on the VCF 4.2 definition are URL encoded.
The following characters are replaced:
% -> %25; 	 -> %09;
 -> %0A;

-> %0D; -> %20; , -> %2C; ; -> %3B; = -> %3D;

Mandatory parameters:
  -bed <file>       BED file used as source of annotations (name column).
  -name <string>    Annotation name in INFO column of output VCF file.

Optional parameters:
  -in <file>        Input VCF file. If unset, reads from STDIN.
                    Default value: ''
  -out <file>       Output VCF list. If unset, writes to STDOUT.
                    Default value: ''
  -sep <string>     Separator used if there are several matches for one variant.
                    Default value: ':'
  -threads <int>    The number of threads used to read, process and write files.
                    Default value: '1'
  -block_size <int> Number of lines processed in one chunk.
                    Default value: '5000'
  -prefetch <int>   Maximum number of chunks that may be pre-fetched into memory.
                    Default value: '64'
  -debug <int>      Enables debug output at the given interval in milliseconds (disabled by default, cannot be combined with writing to STDOUT).
                    Default value: '-1'

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'.

VcfAnnotateFromBed changelog

VcfAnnotateFromBed 2021_06-89-gbbd16264

2021-09-18 Prefetch only part of input file (to save memory).
2021-08-24 Added multithread support.
2021-06-15 Added 'sep' parameter.
2019-12-06 Added URL encoding for INFO values.
2017-03-14 Initial implementation.

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