6 | Command | Description |
     7 |:--------|:------------|
     8 | trim | Trim reads in aligned BAMs |
     9 | variants | Call variants from aligned BAM file |
    10 | filtervariants | Filter variants across replicates
    11 | consensus | Call consensus from aligned BAM file |
    12 | getmasked | Get amplicons with primer mismatches |
    13 | removereads | Remove reads from trimmed BAM file |
    14 | version | Show version information |
    15 | trimadapter | (EXPERIMENTAL) Trim adapter sequences from reads |
    17 To view detailed usage for each command type `ivar <command>`
    18 Note : Commands maked (EXPERIMENTAL) are still under active development.
    20 ## Description of commands
    22 #### Trim primer sequences with iVar
    28 Usage: ivar trim -i <input.bam> -b <primers.bed> -p prefix [-m <min-length>] [-q <min-quality>] [-s <sliding-window-width>]
    30 Input Options    Description
    31            -i    (Required) <input.bam> Indexed aligned bam file to trim primers and quality
    32            -b    (Required) <primers.bed> BED file with primer sequences and positions
    33            -m    Minimum length of read to retain after trimming (Default: 30)
    34            -q    Minimum quality threshold for sliding window to pass (Default: 20)
    35            -s    Width of sliding window (Default: 4)
    37 Output Options   Description
    38            -p    (Required) Prefix for the output BAM file
    46 #### Call variants with iVar
    52 Usage: samtools mpileup -A -d 300000 --reference <reference-fasta> -Q 0 -F 0 <input-bam> | ivar variants -p prefix [-q <min-quality>] [-t <min-frequency-threshold>]
    54 Note : samtools mpileup output must be piped into ivar variants
    56 Input Options    Description
    57            -q    <min-quality> Minimum quality threshold to count base (Default: 20)
    58            -t    <min-frequency-threshold> Minimum frequency threshold(0 - 1) to call variants (Default: 0.03)
    60 Output Options   Description
    61            -p    (Required) Prefix, prefix for the output tsv variant file
    69 #### Filter variants across replicates with iVar
    74 Usage: ivar filtervariants [-p prefix] replicate-one.tsv replicate-two.csv ...
    76 Output Options   Description
    77            -p    (Required) Prefix, prefix for the filtered tsv file
    86 #### Call a consensus sequences from an aligned BAM file.
    91 Usage: samtools mpileup -A -d 300000 -Q 0 -F 0 [<input-bam>] | ivar consensus [-p prefix]
    93 Note : samtools mpileup output must be piped into "ivar consensus"
    95 Input Options    Description
    96            -q    Minimum quality threshold to count base (Default: 20)
    97            -t    Threshold(0 - 100) to call consensus (Default: 0)
    98 Output Options   Description
    99            -p    (Required) Prefix, prefix for the output tsv file
   107 #### Get primers with mismatches to the reference sequence.
   112 Usage: ivar getmasked [-i <input-filtered-tsv>] [-b <bed-file>]
   114 Input Options    Description
   115            -i    (Required) Input filtered variants tsv generated from "ivar filtervariants"
   116            -b    (Required) Bed file with primer indices
   124 #### Remove reads associated with mismatched primer indices
   129 Usage: ivar removereads [-i <input-bam>] [-p prefix] primer-index-1 primer-index-2 primer-index-3 primer-index-4 ...
   131 Input Options    Description
   132            -i    (Required) Input BAM file run through `ivar trim` command whcih adds the primer number to BAM auxillary data
   133 Output Options   Description
   134            -p    (Required) Prefix, prefix for the filtered BAM file