.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.15. .TH IVAR "1" "May 2020" "ivar 1.2.2" "User Commands" .SH NAME ivar \- functions broadly useful for viral amplicon-based sequencing .SH SYNOPSIS .B ivar [\fI\,command \/\fR] .SH 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. .SH COMMANS .TP trim Trim reads in aligned BAM file .TP variants Call variants from aligned BAM file .TP filtervariants Filter variants across replicates or samples .TP consensus Call consensus from aligned BAM file .TP getmasked Detect primer mismatches and get primer indices for the amplicon to be masked .TP removereads Remove reads from trimmed BAM file .TP version Show version information .PP To view detailed usage for each command type `ivar ` .SH AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.