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VcfFilter tool help

VcfFilter (2018_11-7-g60f117b)

Filters a VCF based on the given criteria.

Missing annotation in the SAMPLE filter are treated as passing the filter.
INFO flags (i.e. entries without value) are ignored, i.e. they cannot be filtered.

Optional parameters:
  -in <file>             Input VCF file. If unset, reads from STDIN.
                         Default value: ''
  -out <file>            Output VCF list. If unset, writes to STDOUT.
                         Default value: ''
  -reg <string>          Region of interest in BED format, or comma-separated list of region, e.g. 'chr1:454540-454678,chr2:473457-4734990'.
                         Default value: ''
  -variant_type <string> Filters by variant type. Possible types are: 'snp','indel','multi-allelic','other'.
                         Default value: ''
  -id <string>           Filter by ID column (regular expression).
                         Default value: ''
  -qual <float>          Filter by QUAL column (minimum).
                         Default value: '0'
  -filter <string>       Filter by FILTER column (regular expression).
                         Default value: ''
  -filter_empty          Removes entries with non-empty FILTER column.
                         Default value: 'false'
  -info <string>         Filter by INFO column entries - use ';' as separator for several filters, e.g. 'DP > 5;AO > 2' (spaces are important).
Valid operations are '>','>=','=','!=','<=','<','is','not','contains'.
                         Default value: ''
  -sample <string>       Filter by sample-specific entries - use ';' as separator for several filters, e.g. 'GT is 1/1' (spaces are important).
Valid operations are '>','>=','=','!=','<=','<','is','not','contains'.
                         Default value: ''
  -sample_one_match      If set, a line will pass if one sample passes all filters (default behaviour is that all samples have to pass all filters).
                         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'.

VcfFilter changelog

VcfFilter 2018_11-7-g60f117b

2018-10-31 Initial implementation.

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