---
name: "ivar"
section: "1"
platform: "linux"
package: "ivar"
version: "1.4.4+dfsg-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ivar"
---

# ivar(1)

functions broadly useful for viral amplicon-based sequencing

## NAME

ivar - functions broadly useful for viral amplicon-based sequencing

## SYNOPSIS

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

## DESCRIPTION

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.

## COMMANS

- trim

  Trim reads in aligned BAM file

- variants

  Call variants from aligned BAM file

- filtervariants

  Filter variants across replicates or samples

- consensus

  Call consensus from aligned BAM file

- getmasked

  Detect primer mismatches and get primer indices for the amplicon to be masked

- removereads

  Remove reads from trimmed BAM file

- version

  Show version information

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

## AUTHOR

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