VariantQC.md

VariantQC tool help

VariantQC (2025_09-112-ga53ff6f3d)

Calculates QC metrics on variant lists.

Mandatory parameters:
  -in <file>          Input variant list in VCF format.

Optional parameters:
  -ignore_filter      Ignore filter entries, i.e. consider variants that did not pass filters.
                      Default value: 'false'
  -out <file>         Output qcML file. If unset, writes to STDOUT.
                      Default value: ''
  -txt                Writes TXT format instead of qcML.
                      Default value: 'false'
  -long_read          Adds LongRead specific QC values (e.g. phasing information)
                      Default value: 'false'
  -phasing_bed <file> Output BED file containing phasing blocks with id. (requires parameter '-longread')
                      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).

VariantQC changelog

VariantQC 2025_09-112-ga53ff6f3d

2025-10-21 Added parameter support for dbSNP IDs from INFO entry 'RS' in addition to INFO entry 'CSQ'.
2023-09-21 Added parameter 'longread' to add longread specific QC values.
2020-08-07 VCF files only as input format for variant list.
2018-09-12 Now supports VEP CSQ annotations (no longer support SnpEff ANN annotations).
2017-01-05 Added 'ignore_filter' flag.

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