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1 <tool id="allele_counts_1" version="1.1" name="Variant Annotator">
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2 <description> process variant counts</description>
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3 <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt</command>
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4 <inputs>
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5 <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/>
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6 <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold (in percent)"/>
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7 <param name="covg" type="integer" value="10" min="0" label="Coverage threshold (in reads per strand)"/>
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8 <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" />
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9 <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" />
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10 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" />
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11 </inputs>
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12 <outputs>
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13 <data name="output" format="tabular"/>
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14 </outputs>
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15 <stdio>
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16 <exit_code range="1:" err_level="fatal"/>
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17 <exit_code range=":-1" err_level="fatal"/>
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18 </stdio>
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19
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20 <help>
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21
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22 .. class:: infomark
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23
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24 **What it does**
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25
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26 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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4
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27
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28 -----
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29
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30 .. class:: infomark
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31
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32 **Input Format**
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33
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34 .. class:: warningmark
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35
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36 **Note:** variants that are not A/C/G/T SNVs will be ignored!
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37
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38 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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39
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40 0/0:1:0.02:+T=27,+G=1,-T=22,
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41
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42 -----
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43
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44 .. class:: infomark
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45
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46 **Output**
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47
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48 Each row represents one site in one sample. For unstranded output, 12 fields give information about that site::
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49
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50 1. SAMPLE - Sample name (from VCF sample column labels)
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51 2. CHR - Chromosome of the site
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52 3. POS - Chromosomal coordinate of the site
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53 4. A - Number of reads supporting an 'A'
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54 5. C - 'C' reads
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55 6. G - 'G' reads
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56 7. T - 'T' reads
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57 8. CVRG - Total (number of reads supporting one of the four bases above)
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58 9. ALLELES - Number of qualifying alleles
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59 10. MAJOR - Major allele
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60 11. MINOR - Minor allele (2nd most prevalent variant)
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61 12. MINOR.FREQ.PERC. - Frequency of minor allele
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62
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63 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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64
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65 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
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66 SAMPLE CHR POS +A +C +G +T -A -C -G -T CVRG ALLELES MAJOR MINOR MINOR.FREQ.PERC.
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67
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68 **Example**
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69
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70 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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71
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72 #SAMPLE CHR POS A C G T CVRG ALLELES MAJOR MINOR MINOR.FREQ.PERC.
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73 BLOOD_1 chr20 99 0 101 1 2 104 1 C T 0.01923
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74 BLOOD_2 chr20 99 82 44 0 1 127 2 A C 0.34646
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75 BLOOD_3 chr20 99 0 110 1 0 111 1 C G 0.009
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76 BLOOD_1 chr20 100 3 5 100 0 108 1 G C 0.0463
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77 BLOOD_3 chr20 100 1 118 11 0 130 0 C G 0.08462
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78
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79 -----
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80
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81 .. class:: warningmark
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82
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83 **Site printing and allele tallying requirements**
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84
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85 Coverage threshold:
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86
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87 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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88
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89 Frequency threshold:
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90
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91 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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92
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93 Strand bias:
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94
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95 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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96
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97 </help>
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98
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99 </tool> |
