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VcfFilter tool help

VcfFilter (2024_08-110-g317f43b9)

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: ''
  -remove_invalid          Removes invalid variants, i.e. invalid position of ref/alt.
                           Default value: 'false'
  -remove_non_ref          Remove '<NON_REF>' entries (used in gVCF files).
                           Default value: 'false'
  -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 - keep matches (regular expression).
                           Default value: ''
  -filter_exclude <string> Filter by FILTER column - exclude matches (regular expression).
                           Default value: ''
  -filter_clear            Remove filter entries of all variants, i.e. sets filter to PASS.
                           Default value: 'false'
  -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'
  -no_special_chr          Removes variants that are on special chromosomes, i.e. not on autosomes, not on gonosomes and not on chrMT.
                           Default value: 'false'
  -ref <file>              Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                           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).

VcfFilter changelog

VcfFilter 2024_08-110-g317f43b9

2024-07-11 Added flag 'filter_clear'.
2023-11-21 Added flag 'no_special_chr'.
2018-10-31 Initial implementation.

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