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IVAR(1) User Commands IVAR(1)


ivar - functions broadly useful for viral amplicon-based sequencing


ivar [command <trim|variants|filtervariants|consensus|getmasked|removereads|version|help>]


iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar. While each of these functions can be accomplished using existing tools, iVar contains an intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.


Trim reads in aligned BAM file
Call variants from aligned BAM file
Filter variants across replicates or samples
Call consensus from aligned BAM file
Detect primer mismatches and get primer indices for the amplicon to be masked
Remove reads from trimmed BAM file
Show version information

To view detailed usage for each command type `ivar <command>`


This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.

May 2020 ivar 1.2.2