IVAR(1)

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.