VcfSort.md

VcfSort tool help

VcfSort (2026_06-46-g72aab0308)

Sorts variant lists according to chromosomal position.

Mandatory parameters:
  -in <file>               Input variant list in VCF format.
  -out <file>              Output variant list in VCF or VCF.GZ format.

Optional parameters:
  -compression_level <int> Output VCF compression level from 1 (fastest) to 9 (best compression). If unset, an unzipped VCF is written.
                           Default value: '10'
  -remove_unused_contigs   Remove comment lines of contigs, i.e. chromosomes, that are not used in the output VCF.
                           Default value: 'false'
  -split_chrs              Mode with reduced memory consumption for large files. Sorts only one chromosome at a time into a tmp file and merges all tmp files at the end.
                           Default value: 'false'
  -debug                   Enable debug output to STDOUT.
                           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).

VcfSort changelog

VcfSort 2026_06-46-g72aab0308

2026-06-23 Added parameter '-split_chrs'. Removed parameters 'qual' and 'fai'.
2022-12-08 Added parameter '-remove_unused_contigs'.
2020-08-12 Added parameter '-compression_level' for compression level of output VCF files.

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