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.