fgbio

Tools for working with genomic and high throughput sequencing data.

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UpdateVcfContigNames

Overview

Group: VCF/BCF

Updates then contig names in a VCF.

The name of each sequence must match one of the names (including aliases) in the given sequence dictionary. The new name will be the primary (non-alias) name in the sequence dictionary.

Arguments

Name Flag Type Description Required? Max # of Values Default Value(s)
input i PathToVcf Input VCF. Required 1  
dict d PathToSequenceDictionary The path to the sequence dictionary with contig aliases. Required 1  
output o PathToVcf Output VCF. Required 1  
skip-missing   Boolean Skip missing contigs. Optional 1 false