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VcfAnnotateFromVcf tool help

VcfAnnotateFromVcf (2022_04-120-g0b2ddab9)

Annotates a VCF file with data from one or more source VCF files.

Optional parameters:
  -in <file>             Input VCF(.GZ) file that is annotated. If unset, reads from STDIN.
                         Default value: ''
  -out <file>            Output VCF file. If unset, writes to STDOUT.
                         Default value: ''
  -config_file <file>    TSV file for annotation from multiple source files. For each source file, these tab-separated columns have to be given: source file name, prefix, INFO keys, ID column.
                         Default value: ''
  -source <file>         Tabix indexed VCF.GZ file that is the source of the annotated data.
                         Default value: ''
  -info_keys <string>    INFO key(s) in 'source' that should be annotated (Multiple keys are be separated by ',', optional keys can be renamed using this syntax: 'original_key=new_key').
                         Default value: ''
  -id_column <string>    ID column in 'source' (must be 'ID'). If unset, the ID column is not annotated. Alternative output name can be specified by using 'ID=new_name'.
                         Default value: ''
  -prefix <string>       Prefix added to all annotations in the output VCF file.
                         Default value: ''
  -allow_missing_header  If set the execution is not aborted if a INFO header is missing in the source file.
                         Default value: 'false'
  -threads <int>         The number of threads used to process VCF lines.
                         Default value: '1'
  -block_size <int>      Number of lines processed in one chunk.
                         Default value: '10000'
  -prefetch <int>        Maximum number of chunks that may be pre-fetched into memory.
                         Default value: '64'
  -debug                 Enables debug output (use only with one thread).
                         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'.

VcfAnnotateFromVcf changelog

VcfAnnotateFromVcf 2022_04-120-g0b2ddab9

2022-07-08 Usability: changed parameter names and updated documentation.
2022-02-24 Refactoring and change to event-driven implementation (improved scaling with many threads)
2021-09-20 Prefetch only part of input file (to save memory).
2020-04-11 Added multithread support.
2019-08-19 Added support for multiple annotations files through config file.
2019-08-14 Added VCF.GZ support.
2019-08-13 Initial implementation.

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