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UpdHunter tool help

UpdHunter (2023_11-42-ga9d1687d)

UPD detection from trio variant data.

Mandatory parameters:
  -in <file>               Input VCF file of trio.
  -c <string>              Header name of child.
  -f <string>              Header name of father.
  -m <string>              Header name of mother.
  -out <file>              Output TSV file containing the detected UPDs.

Optional parameters:
  -out_informative <file>  Output IGV file containing informative variants.
                           Default value: ''
  -exclude <file>          BED file with regions to exclude, e.g. copy-number variant regions.
                           Default value: ''
  -var_min_dp <int>        Minimum depth (DP) of a variant (in all three samples).
                           Default value: '20'
  -var_min_q <float>       Minimum quality (QUAL) of a variant.
                           Default value: '30'
  -var_use_indels          Also use InDels. The default is to use SNVs only.
                           Default value: 'false'
  -ext_marker_perc <float> Percentage of markers that can be spanned when merging adjacent regions .
                           Default value: '1'
  -ext_size_perc <float>   Percentage of base size that can be spanned when merging adjacent regions.
                           Default value: '20'
  -reg_min_kb <float>      Mimimum size in kilo-bases required for a UPD region.
                           Default value: '1000'
  -reg_min_markers <int>   Mimimum number of UPD markers required in a region.
                           Default value: '15'
  -reg_min_q <float>       Mimimum Q-score required for a UPD region.
                           Default value: '20'
  -debug                   Enable verbose debug output.
                           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'.

UpdHunter changelog

UpdHunter 2023_11-42-ga9d1687d

2024-06-06 Added optional output file containing informative variants.
2020-08-07 VCF files only as input format for variant list.
2018-06-11 First working version.

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