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VcfStreamSort tool help

VcfStreamSort (2024_08-113-g94a3b440)

Sort entries of a VCF file according to genomic position using a stream. Variants must be grouped by chromosome!

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: ''
  -n <int>          Number of variants to cache for sorting.
                    Default value: '10000'

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).

VcfStreamSort changelog

VcfStreamSort 2024_08-113-g94a3b440

2019-01-08 Added REF, ALT and INFO fields to sorting for a defined output order.
2016-06-27 Initial implementation.

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