Skip to content

Latest commit

 

History

History
34 lines (28 loc) · 1.83 KB

VcfLeftNormalize.md

File metadata and controls

34 lines (28 loc) · 1.83 KB
Raw

VcfLeftNormalize tool help

VcfLeftNormalize (2024_08-110-g317f43b9)

Normalizes all variants and shifts indels to the left in a VCF file.

Note: Multi-allelic variants, SNVs, MNPs, complex InDels and invalid variants are skipped!

Optional parameters:
  -in <file>               Input VCF or VCF.GZ 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'
  -right                   Right-normalize VCF instead of left-normalizing it.
                           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).

VcfLeftNormalize changelog

VcfLeftNormalize 2024_08-110-g317f43b9

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

back to ngs-bits