Biowulf High Performance Computing at the NIH
iVar: iVar: a tool for viral amplicon-based sequencing.

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.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn4471 ~]$ module load ivar 
[+] Loading samtools 1.9  ...
[+] Loading ivar 1.3.1  ...
Copy sample data to your current folder:
[user@cn4471 ~]$ cp $IVAR_DATA/* .
[user@cn4471 ~]$ cp test_amplicon.sorted.bam test.bam 
Preprocess the data with samtools: [user@cn4471 ~]$ samtools sort -o test.sorted.bam test.bam [user@cn4471 ~]$ samtools index test.sorted.bam iVar can be used as follows:
[user@cn4471 ~]$ ivar -h
Usage:  ivar [command <trim|callvariants|filtervariants|consensus|getmasked|removereads|version|help>]

        Command       Description
           trim       Trim reads in aligned BAM file
       variants       Call variants from aligned BAM file
 filtervariants       Filter variants across replicates
      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>, for example:
[user@cn4471 ~]$ ivar trim -h 
Usage: ivar trim -i <input.bam> -b <primers.bed> -p <prefix> [-m <min-length>] [-q <min-quality>] [-s <sliding-window-width>]
Input Options    Description
           -i    (Required) Sorted bam file, with aligned reads, to trim primers and quality
           -b    (Required) BED file with primer sequences and positions
           -m    Minimum length of read to retain after trimming (Default: 30)
           -q    Minimum quality threshold for sliding window to pass (Default: 20)
           -s    Width of sliding window (Default: 4)
           -e    Include reads with no primers. By default, reads with no primers are excluded
Output Options   Description
           -p    (Required) Prefix for the output BAM file
Perform the trimming on sample data:
[user@cn4471 ~]$ cp test_isize.bed test_primers.bed 
[user@cn4471 ~]$ ivar trim -b test_primers.bed -p test.trimmed -i test.bam -q 15 -m 50 -s 4 
Found 218 primers in BED file
Amplicons detected:

Number of references in file: 1
NC_045512.2
Using Region: NC_045512.2

Found 8 mapped reads
Found 0 unmapped reads
Sorted By Coordinate
-------
Processed 10% reads ...
Processed 20% reads ...
Processed 30% reads ...
Processed 40% reads ...

-------
Results:
Primer Name     Read Count
nCoV-2019_1_LEFT        0
nCoV-2019_1_RIGHT       0
nCoV-2019_2_LEFT        0
nCoV-2019_2_RIGHT       0
nCoV-2019_3_LEFT        0
nCoV-2019_3_RIGHT       0
nCoV-2019_4_LEFT        0
nCoV-2019_4_RIGHT       0
...
nCoV-2019_96_LEFT       0
nCoV-2019_96_RIGHT      0
nCoV-2019_97_LEFT       0
nCoV-2019_97_RIGHT      0
nCoV-2019_98_LEFT       0
nCoV-2019_98_RIGHT      0

Trimmed primers from 100% (8) of reads.
0% (0) of reads were quality trimmed below the minimum length of 50 bp and were not written to file.
0% (0) of reads that started outside of primer regions were not written to file
50% (4) of reads had their insert size smaller than their read length
End the interactive session:
[user@cn4471 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$