UpdHunter (2020_03-260-ge35d12de)
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:
-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 2020_03-260-ge35d12de
2020-08-07 VCF files only as input format for variant list.
2018-06-11 First working version.