VcfCheck.md

VcfCheck tool help

VcfCheck (2025_05-79-g6c060cfd)

Checks a VCF file for errors.

Checks the input VCF file with SNVs and small InDels for errors and warnings.
If the VEP-based CSQ annotation is present, it also checks that the Miso terms in the consequence field are valid.

Optional parameters:
  -in <file>        Input VCF file. If unset, reads from STDIN.
                    Default value: ''
  -out <file>       Output file. If unset, writes to STDOUT.
                    Default value: ''
  -lines <int>      Number of variant lines to check in the VCF file (unlimited if 0)
                    Default value: '5000'
  -ref <file>       Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                    Default value: ''
  -info             Add general information about the input file to the output.
                    Default value: 'false'
  -duplicates       Check for variants occuring twice (input VCF needs to be sorted).
                    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'.
  --settings [file] Settings override file (no other settings files are used).

VcfCheck changelog

VcfCheck 2025_05-79-g6c060cfd

2025-05-30 Added parameter 'duplicates'.
2019-12-13 Added support for gzipped VCF files.
2019-12-11 Added check for invalid characters in INFO column.
2018-12-03 Initial implementation.

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