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annotate allele-counts.xml @ 9:6cc488e11544 draft

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"planemo upload for repository https://github.com/galaxyproject/dunovo commit 5a2e08bc1213b0437d0adcb45f7f431bd3c735f4"
author nick
date Tue, 31 Mar 2020 05:09:12 -0400
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1 <tool id="allele_counts_1" version="1.3" name="Variant Annotator">
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2 <description> process variant counts</description>
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3 <stdio>
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4 <exit_code range="1:" level="fatal" />
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5 <exit_code range=":-1" level="fatal" />
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6 </stdio>
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7 <command>allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt
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8 #if $seed:
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9 -r $seed
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10 #end if
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11 </command>
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12 <inputs>
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13 <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/>
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14 <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/>
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15 <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/>
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16 <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" />
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17 <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" />
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18 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" />
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19 <param name="seed" type="text" value="" label="PRNG seed" />
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20 </inputs>
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21 <outputs>
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22 <data name="output" format="tabular" />
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23 </outputs>
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24
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25 <tests>
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26 <test>
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27 <param name="input" value="tests/artificial.vcf.in" />
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28 <param name="freq" value="10" />
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29 <param name="covg" value="10" />
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30 <param name="seed" value="1" />
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31 <output name="output" file="tests/artificial.csv.out" />
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32 </test>
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33 </tests>
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34
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35 <help>
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36
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37 .. class:: infomark
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38
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39 **What it does**
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40
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41 This tool parses variant counts from a special VCF file. It counts simple variants, calculates numbers of alleles, and calculates minor allele frequency. It can apply filters based on coverage, strand bias, and minor allele frequency cutoffs.
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42
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43 -----
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44
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45 .. class:: infomark
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46
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47 **Input Format**
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48
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49 .. class:: warningmark
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50
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51 **Note:** variants that are not A/C/G/T SNVs will be ignored!
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52
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53 The input VCF should be like the output of the **Naive Variant Detector** tool (using the stranded option). The sample column(s) must give the read count for each variant **on each strand**. Below is an example of a valid sample column entry (the important part is after the last colon)::
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54
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55 0/0:1:0.02:+T=27,+G=1,-T=22,
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56
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57 -----
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58
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59 .. class:: infomark
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60
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61 **Output**
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62
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63 Each row represents one site in one sample. For **unstranded** output, 13 fields give information about that site::
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64
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65 1. SAMPLE - Sample name (from VCF sample column labels)
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66 2. CHR - Chromosome of the site
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67 3. POS - Chromosomal coordinate of the site
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68 4. A - Number of reads supporting an 'A'
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69 5. C - 'C' reads
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70 6. G - 'G' reads
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71 7. T - 'T' reads
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72 8. CVRG - Total (number of reads supporting one of the four bases above)
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73 9. ALLELES - Number of qualifying alleles
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74 10. MAJOR - Major allele
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75 11. MINOR - Minor allele (2nd most prevalent variant)
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76 12. MAF - Frequency of minor allele
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77 13. BIAS - Strand bias measure
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78
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79 For stranded output, instead of using 4 columns to report read counts per base, 8 are used to report the stranded counts per base::
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80
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81 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17
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82 SAMPLE CHR POS +A +C +G +T -A -C -G -T CVRG ALLELES MAJOR MINOR MAF BIAS
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83
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84 **Example**
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85
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86 Below is a header line, followed by some example data lines. Since the input contained three samples, the data for each site is reported on three consecutive lines. However, if a sample fell below the coverage threshold at that site, the line will be omitted::
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87
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88 #SAMPLE CHR POS A C G T CVRG ALLELES MAJOR MINOR MAF BIAS
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89 BLOOD_1 chr20 99 0 101 1 2 104 1 C T 0.01923 0.33657
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90 BLOOD_2 chr20 99 82 44 0 1 127 2 A C 0.34646 0.07823
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91 BLOOD_3 chr20 99 0 110 1 0 111 1 C G 0.009 1.00909
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92 BLOOD_1 chr20 100 3 5 100 0 108 1 G C 0.0463 0.15986
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93 BLOOD_3 chr20 100 1 118 11 0 130 0 C G 0.08462 0.04154
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94
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95 -----
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96
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97 .. class:: warningmark
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98
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99 **Site printing and allele tallying requirements**
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100
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101 Coverage threshold:
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102
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103 If a coverage threshold is used, the number of reads **on each strand** must be at or above the threshold. If either strand is below the threshold, the line will be omitted. **N.B.** this means the total coverage for each printed site will be at least twice the number you give in the "coverage threshold" option. Also, since only simple variants are counted, a site with 100 reads, all supporting a deletion variant, would not be printed.
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104
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105 Frequency threshold:
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106
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107 If a frequency threshold is used, alleles are only counted (in the ALLELES column) if they meet or exceed this minor allele frequency threshold.
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108
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109 Strand bias:
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110
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111 The alleles passing the threshold on each strand must match (though not in order), or the allele count will be 0. So a site with A, C, G on the plus strand and A, G on the minus strand will get an allele count of zero, though the (strand-independent) major allele, minor allele, and minor allele frequency will still be reported. If there is a tie for the minor allele, one will be randomly chosen.
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112
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113 Additionally, a measure of strand bias is given in the last column. This is calculated using the method of Guo et al., 2012. A value of "." is given when there is no valid result of the calculation due to a zero denominator. This occurs when there are no reads on one of the strands, or when there is no minor allele.
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114
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115 </help>
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116
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117 <citations>
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118 <citation type="bibtex">
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119 @article{Blankenberg2014,
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120 author = {Blankenberg, Daniel and {Von Kuster}, Gregory and Bouvier, Emil and Baker, Dannon and Afgan, Enis and Stoler, Nicholas and Taylor, James and Nekrutenko, Anton},
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121 doi = {10.1186/gb4161},
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122 issn = {1465-6906},
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123 journal = {Genome Biology},
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124 keywords = {galaxy},
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125 number = {2},
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126 pages = {403},
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127 title = {{Dissemination of scientific software with Galaxy ToolShed}},
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128 url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb4161},
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129 volume = {15},
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130 year = {2014}
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131 }
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132 </citation>
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133 <citation type="bibtex">
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134 @article{Dickins2014,
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135 archivePrefix = {arXiv},
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136 arxivId = {15334406},
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137 author = {Dickins, Benjamin and Rebolledo-Jaramillo, Boris and Su, Marcia Shu Wei and Paul, Ian M and Blankenberg, Daniel and Stoler, Nicholas and Makova, Kateryna D and Nekrutenko, Anton},
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138 doi = {10.2144/000114146},
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139 eprint = {15334406},
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140 isbn = {5049880467},
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141 issn = {19409818},
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142 journal = {BioTechniques},
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143 number = {3},
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144 pages = {134--141},
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145 pmid = {24641477},
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146 title = {{Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach}},
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147 volume = {56},
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148 year = {2014}
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149 }
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150 </citation>
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151 </citations>
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152
6
df3b28364cd2 allele-counts.{py,xml}: Add strand bias, documentation updates.
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153 </tool>