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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno"> 1</span> Manual {#mainpage}</div><div class="line"><a name="l00002"></a><span class="lineno"> 2</span> ============</div><div class="line"><a name="l00003"></a><span class="lineno"> 3</span> </div><div class="line"><a name="l00004"></a><span class="lineno"> 4</span> ## Available Commands</div><div class="line"><a name="l00005"></a><span class="lineno"> 5</span> </div><div class="line"><a name="l00006"></a><span class="lineno"> 6</span> | Command | Description |</div><div class="line"><a name="l00007"></a><span class="lineno"> 7</span> |:--------|:------------|</div><div class="line"><a name="l00008"></a><span class="lineno"> 8</span> | trim | Trim reads in aligned BAMs |</div><div class="line"><a name="l00009"></a><span class="lineno"> 9</span> | variants | Call variants from aligned BAM file |</div><div class="line"><a name="l00010"></a><span class="lineno"> 10</span> | filtervariants | Filter variants across replicates</div><div class="line"><a name="l00011"></a><span class="lineno"> 11</span> | consensus | Call consensus from aligned BAM file |</div><div class="line"><a name="l00012"></a><span class="lineno"> 12</span> | getmasked | Get amplicons with primer mismatches |</div><div class="line"><a name="l00013"></a><span class="lineno"> 13</span> | removereads | Remove reads from trimmed BAM file |</div><div class="line"><a name="l00014"></a><span class="lineno"> 14</span> | version | Show version information |</div><div class="line"><a name="l00015"></a><span class="lineno"> 15</span> | trimadapter | (EXPERIMENTAL) Trim adapter sequences from reads |</div><div class="line"><a name="l00016"></a><span class="lineno"> 16</span> </div><div class="line"><a name="l00017"></a><span class="lineno"> 17</span> To view detailed usage for each command type `ivar <command>`</div><div class="line"><a name="l00018"></a><span class="lineno"> 18</span> Note : Commands maked (EXPERIMENTAL) are still under active development.</div><div class="line"><a name="l00019"></a><span class="lineno"> 19</span> </div><div class="line"><a name="l00020"></a><span class="lineno"> 20</span> ## Description of commands</div><div class="line"><a name="l00021"></a><span class="lineno"> 21</span> </div><div class="line"><a name="l00022"></a><span class="lineno"> 22</span> #### Trim primer sequences with iVar</div><div class="line"><a name="l00023"></a><span class="lineno"> 23</span> </div><div class="line"><a name="l00024"></a><span class="lineno"> 24</span> Command:</div><div class="line"><a name="l00025"></a><span class="lineno"> 25</span> ```</div><div class="line"><a name="l00026"></a><span class="lineno"> 26</span> ivar trim</div><div class="line"><a name="l00027"></a><span class="lineno"> 27</span> </div><div class="line"><a name="l00028"></a><span class="lineno"> 28</span> Usage: ivar trim -i <input.bam> -b <primers.bed> -p prefix [-m <min-length>] [-q <min-quality>] [-s <sliding-window-width>]</div><div class="line"><a name="l00029"></a><span class="lineno"> 29</span> </div><div class="line"><a name="l00030"></a><span class="lineno"> 30</span> Input Options Description</div><div class="line"><a name="l00031"></a><span class="lineno"> 31</span>  -i (Required) <input.bam> Indexed aligned bam file to trim primers and quality</div><div class="line"><a name="l00032"></a><span class="lineno"> 32</span>  -b (Required) <primers.bed> BED file with primer sequences and positions</div><div class="line"><a name="l00033"></a><span class="lineno"> 33</span>  -m Minimum length of read to retain after trimming (Default: 30)</div><div class="line"><a name="l00034"></a><span class="lineno"> 34</span>  -q Minimum quality threshold for sliding window to pass (Default: 20)</div><div class="line"><a name="l00035"></a><span class="lineno"> 35</span>  -s Width of sliding window (Default: 4)</div><div class="line"><a name="l00036"></a><span class="lineno"> 36</span> </div><div class="line"><a name="l00037"></a><span class="lineno"> 37</span> Output Options Description</div><div class="line"><a name="l00038"></a><span class="lineno"> 38</span>  -p (Required) Prefix for the output BAM file</div><div class="line"><a name="l00039"></a><span class="lineno"> 39</span> ```</div><div class="line"><a name="l00040"></a><span class="lineno"> 40</span> </div><div class="line"><a name="l00041"></a><span class="lineno"> 41</span> Example Usage:</div><div class="line"><a name="l00042"></a><span class="lineno"> 42</span> ```</div><div class="line"><a name="l00043"></a><span class="lineno"> 43</span> </div><div class="line"><a name="l00044"></a><span class="lineno"> 44</span> ```</div><div class="line"><a name="l00045"></a><span class="lineno"> 45</span> </div><div class="line"><a name="l00046"></a><span class="lineno"> 46</span> #### Call variants with iVar</div><div class="line"><a name="l00047"></a><span class="lineno"> 47</span> </div><div class="line"><a name="l00048"></a><span class="lineno"> 48</span> Command:</div><div class="line"><a name="l00049"></a><span class="lineno"> 49</span> ```</div><div class="line"><a name="l00050"></a><span class="lineno"> 50</span> ivar variants</div><div class="line"><a name="l00051"></a><span class="lineno"> 51</span> </div><div class="line"><a name="l00052"></a><span class="lineno"> 52</span> 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>]</div><div class="line"><a name="l00053"></a><span class="lineno"> 53</span> </div><div class="line"><a name="l00054"></a><span class="lineno"> 54</span> Note : samtools mpileup output must be piped into ivar variants</div><div class="line"><a name="l00055"></a><span class="lineno"> 55</span> </div><div class="line"><a name="l00056"></a><span class="lineno"> 56</span> Input Options Description</div><div class="line"><a name="l00057"></a><span class="lineno"> 57</span>  -q <min-quality> Minimum quality threshold to count base (Default: 20)</div><div class="line"><a name="l00058"></a><span class="lineno"> 58</span>  -t <min-frequency-threshold> Minimum frequency threshold(0 - 1) to call variants (Default: 0.03)</div><div class="line"><a name="l00059"></a><span class="lineno"> 59</span> </div><div class="line"><a name="l00060"></a><span class="lineno"> 60</span> Output Options Description</div><div class="line"><a name="l00061"></a><span class="lineno"> 61</span>  -p (Required) Prefix, prefix for the output tsv variant file</div><div class="line"><a name="l00062"></a><span class="lineno"> 62</span> ```</div><div class="line"><a name="l00063"></a><span class="lineno"> 63</span> </div><div class="line"><a name="l00064"></a><span class="lineno"> 64</span> Example Usage:</div><div class="line"><a name="l00065"></a><span class="lineno"> 65</span> ```</div><div class="line"><a name="l00066"></a><span class="lineno"> 66</span> </div><div class="line"><a name="l00067"></a><span class="lineno"> 67</span> ```</div><div class="line"><a name="l00068"></a><span class="lineno"> 68</span> </div><div class="line"><a name="l00069"></a><span class="lineno"> 69</span> #### Filter variants across replicates with iVar</div><div class="line"><a name="l00070"></a><span class="lineno"> 70</span> </div><div class="line"><a name="l00071"></a><span class="lineno"> 71</span> Command:</div><div class="line"><a name="l00072"></a><span class="lineno"> 72</span> ```</div><div class="line"><a name="l00073"></a><span class="lineno"> 73</span> ivar filtervariants</div><div class="line"><a name="l00074"></a><span class="lineno"> 74</span> Usage: ivar filtervariants [-p prefix] replicate-one.tsv replicate-two.csv ...</div><div class="line"><a name="l00075"></a><span class="lineno"> 75</span> </div><div class="line"><a name="l00076"></a><span class="lineno"> 76</span> Output Options Description</div><div class="line"><a name="l00077"></a><span class="lineno"> 77</span>  -p (Required) Prefix, prefix for the filtered tsv file</div><div class="line"><a name="l00078"></a><span class="lineno"> 78</span> </div><div class="line"><a name="l00079"></a><span class="lineno"> 79</span> ```</div><div class="line"><a name="l00080"></a><span class="lineno"> 80</span> </div><div class="line"><a name="l00081"></a><span class="lineno"> 81</span> Example Usage:</div><div class="line"><a name="l00082"></a><span class="lineno"> 82</span> ```</div><div class="line"><a name="l00083"></a><span class="lineno"> 83</span> </div><div class="line"><a name="l00084"></a><span class="lineno"> 84</span> ```</div><div class="line"><a name="l00085"></a><span class="lineno"> 85</span> </div><div class="line"><a name="l00086"></a><span class="lineno"> 86</span> #### Call a consensus sequences from an aligned BAM file.</div><div class="line"><a name="l00087"></a><span class="lineno"> 87</span> </div><div class="line"><a name="l00088"></a><span class="lineno"> 88</span> Command:</div><div class="line"><a name="l00089"></a><span class="lineno"> 89</span> ```</div><div class="line"><a name="l00090"></a><span class="lineno"> 90</span> ivar consensus</div><div class="line"><a name="l00091"></a><span class="lineno"> 91</span> Usage: samtools mpileup -A -d 300000 -Q 0 -F 0 [<input-bam>] | ivar consensus [-p prefix]</div><div class="line"><a name="l00092"></a><span class="lineno"> 92</span> </div><div class="line"><a name="l00093"></a><span class="lineno"> 93</span> Note : samtools mpileup output must be piped into "ivar consensus"</div><div class="line"><a name="l00094"></a><span class="lineno"> 94</span> </div><div class="line"><a name="l00095"></a><span class="lineno"> 95</span> Input Options Description</div><div class="line"><a name="l00096"></a><span class="lineno"> 96</span>  -q Minimum quality threshold to count base (Default: 20)</div><div class="line"><a name="l00097"></a><span class="lineno"> 97</span>  -t Threshold(0 - 100) to call consensus (Default: 0)</div><div class="line"><a name="l00098"></a><span class="lineno"> 98</span> Output Options Description</div><div class="line"><a name="l00099"></a><span class="lineno"> 99</span>  -p (Required) Prefix, prefix for the output tsv file</div><div class="line"><a name="l00100"></a><span class="lineno"> 100</span> ```</div><div class="line"><a name="l00101"></a><span class="lineno"> 101</span> </div><div class="line"><a name="l00102"></a><span class="lineno"> 102</span> Example Usage:</div><div class="line"><a name="l00103"></a><span class="lineno"> 103</span> ```</div><div class="line"><a name="l00104"></a><span class="lineno"> 104</span> </div><div class="line"><a name="l00105"></a><span class="lineno"> 105</span> ```</div><div class="line"><a name="l00106"></a><span class="lineno"> 106</span> </div><div class="line"><a name="l00107"></a><span class="lineno"> 107</span> #### Get primers with mismatches to the reference sequence.</div><div class="line"><a name="l00108"></a><span class="lineno"> 108</span> </div><div class="line"><a name="l00109"></a><span class="lineno"> 109</span> Command:</div><div class="line"><a name="l00110"></a><span class="lineno"> 110</span> ```</div><div class="line"><a name="l00111"></a><span class="lineno"> 111</span> ivar getmasked</div><div class="line"><a name="l00112"></a><span class="lineno"> 112</span> Usage: ivar getmasked [-i <input-filtered-tsv>] [-b <bed-file>]</div><div class="line"><a name="l00113"></a><span class="lineno"> 113</span> </div><div class="line"><a name="l00114"></a><span class="lineno"> 114</span> Input Options Description</div><div class="line"><a name="l00115"></a><span class="lineno"> 115</span>  -i (Required) Input filtered variants tsv generated from "ivar filtervariants"</div><div class="line"><a name="l00116"></a><span class="lineno"> 116</span>  -b (Required) Bed file with primer indices</div><div class="line"><a name="l00117"></a><span class="lineno"> 117</span> ```</div><div class="line"><a name="l00118"></a><span class="lineno"> 118</span> </div><div class="line"><a name="l00119"></a><span class="lineno"> 119</span> Example Usage:</div><div class="line"><a name="l00120"></a><span class="lineno"> 120</span> ```</div><div class="line"><a name="l00121"></a><span class="lineno"> 121</span> </div><div class="line"><a name="l00122"></a><span class="lineno"> 122</span> ```</div><div class="line"><a name="l00123"></a><span class="lineno"> 123</span> </div><div class="line"><a name="l00124"></a><span class="lineno"> 124</span> #### Remove reads associated with mismatched primer indices</div><div class="line"><a name="l00125"></a><span class="lineno"> 125</span> </div><div class="line"><a name="l00126"></a><span class="lineno"> 126</span> Command:</div><div class="line"><a name="l00127"></a><span class="lineno"> 127</span> ```</div><div class="line"><a name="l00128"></a><span class="lineno"> 128</span> ivar removereads</div><div class="line"><a name="l00129"></a><span class="lineno"> 129</span> Usage: ivar removereads [-i <input-bam>] [-p prefix] primer-index-1 primer-index-2 primer-index-3 primer-index-4 ...</div><div class="line"><a name="l00130"></a><span class="lineno"> 130</span> </div><div class="line"><a name="l00131"></a><span class="lineno"> 131</span> Input Options Description</div><div class="line"><a name="l00132"></a><span class="lineno"> 132</span>  -i (Required) Input BAM file run through `ivar trim` command whcih adds the primer number to BAM auxillary data</div><div class="line"><a name="l00133"></a><span class="lineno"> 133</span> Output Options Description</div><div class="line"><a name="l00134"></a><span class="lineno"> 134</span>  -p (Required) Prefix, prefix for the filtered BAM file</div><div class="line"><a name="l00135"></a><span class="lineno"> 135</span> ```</div><div class="line"><a name="l00136"></a><span class="lineno"> 136</span> </div><div class="line"><a name="l00137"></a><span class="lineno"> 137</span> Example Usage:</div><div class="line"><a name="l00138"></a><span class="lineno"> 138</span> ```</div><div class="line"><a name="l00139"></a><span class="lineno"> 139</span> </div><div class="line"><a name="l00140"></a><span class="lineno"> 140</span> ```</div></div><!-- fragment --></div><!-- contents -->
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