ivar1
Functions broadly useful for viral amplicon-based sequencing
Usage
ivar [{command
<trim | variants | filtervariants | consensus | getmasked | removereads | version | help>}]
Overview
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>`
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).