Skip to content

Latest commit

 

History

History
33 lines (27 loc) · 1.37 KB

VcfCheck.md

File metadata and controls

33 lines (27 loc) · 1.37 KB
Raw

VcfCheck tool help

VcfCheck (2023_11-42-ga9d1687d)

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'

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'.

VcfCheck changelog

VcfCheck 2023_11-42-ga9d1687d

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.

back to ngs-bits