Mercurial > repos > nick > allele_counts
annotate allele-counts.xml @ 8:411adeff1eec draft
Handle "." sample columns, update tests to work with BIAS column.
| author | nick |
|---|---|
| date | Tue, 23 Aug 2016 02:30:56 -0400 |
| parents | a72277535a2c |
| children | 6cc488e11544 |
| rev | line source |
|---|---|
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
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1 <tool id="allele_counts_1" version="1.2" name="Variant Annotator"> |
| 5 | 2 <description> process variant counts</description> |
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allele-counts.xml: Fix bug causing crash when no seed is given.
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3 <command interpreter="python">allele-counts.py -i $input -o $output -f $freq -c $covg $header $stranded $nofilt |
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a72277535a2c
allele-counts.xml: Fix bug causing crash when no seed is given.
nicksto <nmapsy@gmail.com>
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4 #if $seed: |
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a72277535a2c
allele-counts.xml: Fix bug causing crash when no seed is given.
nicksto <nmapsy@gmail.com>
parents:
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5 -r $seed |
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a72277535a2c
allele-counts.xml: Fix bug causing crash when no seed is given.
nicksto <nmapsy@gmail.com>
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6 #end if |
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a72277535a2c
allele-counts.xml: Fix bug causing crash when no seed is given.
nicksto <nmapsy@gmail.com>
parents:
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7 </command> |
| 0 | 8 <inputs> |
| 9 <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/> | |
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allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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10 <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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11 <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/> |
| 5 | 12 <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" /> |
| 13 <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" /> | |
| 3 | 14 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" /> |
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allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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15 <param name="seed" type="text" value="" label="PRNG seed" /> |
| 0 | 16 </inputs> |
| 17 <outputs> | |
| 18 <data name="output" format="tabular"/> | |
| 19 </outputs> | |
| 20 <stdio> | |
| 21 <exit_code range="1:" err_level="fatal"/> | |
| 22 <exit_code range=":-1" err_level="fatal"/> | |
| 23 </stdio> | |
| 24 | |
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allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
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25 <tests> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
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26 <test> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
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27 <param name="input" value="tests/artificial.vcf.in" /> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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28 <param name="freq" value="10" /> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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diff
changeset
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29 <param name="covg" value="10" /> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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changeset
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30 <param name="seed" value="1" /> |
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nicksto <nmapsy@gmail.com>
parents:
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31 <output name="output" file="tests/artificial.csv.out" /> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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32 </test> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
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33 </tests> |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
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34 |
| 0 | 35 <help> |
| 3 | 36 |
| 4 | 37 .. class:: infomark |
| 38 | |
| 39 **What it does** | |
| 40 | |
| 5 | 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. |
| 4 | 42 |
| 43 ----- | |
| 44 | |
| 5 | 45 .. class:: infomark |
| 46 | |
| 47 **Input Format** | |
| 48 | |
| 3 | 49 .. class:: warningmark |
| 50 | |
| 5 | 51 **Note:** variants that are not A/C/G/T SNVs will be ignored! |
| 3 | 52 |
| 5 | 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):: |
| 54 | |
| 55 0/0:1:0.02:+T=27,+G=1,-T=22, | |
| 3 | 56 |
| 57 ----- | |
| 58 | |
| 59 .. class:: infomark | |
| 60 | |
| 5 | 61 **Output** |
| 3 | 62 |
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allele-counts.{py,xml}: Add strand bias, documentation updates.
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63 Each row represents one site in one sample. For **unstranded** output, 13 fields give information about that site:: |
| 0 | 64 |
| 5 | 65 1. SAMPLE - Sample name (from VCF sample column labels) |
| 3 | 66 2. CHR - Chromosome of the site |
| 67 3. POS - Chromosomal coordinate of the site | |
| 68 4. A - Number of reads supporting an 'A' | |
| 5 | 69 5. C - 'C' reads |
| 70 6. G - 'G' reads | |
| 71 7. T - 'T' reads | |
| 3 | 72 8. CVRG - Total (number of reads supporting one of the four bases above) |
| 73 9. ALLELES - Number of qualifying alleles | |
| 5 | 74 10. MAJOR - Major allele |
| 75 11. MINOR - Minor allele (2nd most prevalent variant) | |
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allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
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76 12. MAF - Frequency of minor allele |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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77 13. BIAS - Strand bias measure |
| 3 | 78 |
| 5 | 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:: |
| 80 | |
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allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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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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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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82 SAMPLE CHR POS +A +C +G +T -A -C -G -T CVRG ALLELES MAJOR MINOR MAF BIAS |
| 5 | 83 |
| 4 | 84 **Example** |
| 85 | |
| 5 | 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:: |
| 4 | 87 |
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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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88 #SAMPLE CHR POS A C G T CVRG ALLELES MAJOR MINOR MAF BIAS |
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df3b28364cd2
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nicksto <nmapsy@gmail.com>
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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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nicksto <nmapsy@gmail.com>
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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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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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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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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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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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df3b28364cd2
allele-counts.{py,xml}: Add strand bias, documentation updates.
nicksto <nmapsy@gmail.com>
parents:
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93 BLOOD_3 chr20 100 1 118 11 0 130 0 C G 0.08462 0.04154 |
| 3 | 94 |
| 95 ----- | |
| 96 | |
| 97 .. class:: warningmark | |
| 98 | |
| 99 **Site printing and allele tallying requirements** | |
| 100 | |
| 5 | 101 Coverage threshold: |
| 3 | 102 |
| 5 | 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. |
| 3 | 104 |
| 5 | 105 Frequency threshold: |
| 3 | 106 |
| 5 | 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. |
| 3 | 108 |
| 5 | 109 Strand bias: |
| 3 | 110 |
| 5 | 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. |
| 3 | 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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df3b28364cd2
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114 |
| 0 | 115 </help> |
| 116 | |
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117 </tool> |