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VariantQC tool help

VariantQC (2020_06-115-g597ef477)

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'

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'.

VariantQC changelog

VariantQC 2020_06-115-g597ef477

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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