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.