fgbio

Tools for working with genomic and high throughput sequencing data.

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UpdateIntervalListContigNames

Overview

Group: FASTA

Updates the sequence names in an Interval List file.

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.

Use --skip-missing to ignore intervals where a contig name could not be updated (i.e. missing from the sequence dictionary).

Arguments

Name Flag Type Description Required? Max # of Values Default Value(s)
input i PathToIntervals Input interval list. Required 1  
dict d PathToSequenceDictionary The path to the sequence dictionary with contig aliases. Required 1  
output o PathToIntervals Output interval list. Required 1  
skip-missing   Boolean Skip contigs in the interval list that are not found in the sequence dictionary. Optional 1 false