ivar - functions broadly useful for viral amplicon-based sequencing

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

ivar 1.2.2                                          May 2020                                             IVAR(1)

       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>`

       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.

       ivar - functions broadly useful for viral amplicon-based sequencing

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