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VcfLeftNormalize tool help

VcfLeftNormalize (2021_03-23-g5c26fea8)

Normalizes all variants and shifts indels to the left in a VCF file. Multi-allelic and complex variant are not changed!

Optional parameters:
  -in <file>               Input VCF file. If unset, reads from STDIN.
                           Default value: ''
  -out <file>              Output VCF or VCF or VCF.GZ file. If unset, writes to STDOUT.
                           Default value: ''
  -ref <file>              Reference genome FASTA file. If unset 'reference_genome' from the 'settings.ini' file is used.
                           Default value: ''
  -compression_level <int> Output VCF compression level from 1 (fastest) to 9 (best compression). If unset, an unzipped VCF is written.
                           Default value: '10'
  -stream                  Allows to stream the input and output VCF without loading the whole file into memory. Only supported with uncompressed VCF files.
                           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'.

VcfLeftNormalize changelog

VcfLeftNormalize 2021_03-23-g5c26fea8

2020-08-12 Added parameter '-compression_level' for compression level of output vcf files.
2016-06-24 Initial implementation.

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