Mercurial > repos > nick > allele_counts
view allele-counts.xml @ 10:7f19e8c03358 draft
"planemo upload for repository https://github.com/galaxyproject/dunovo commit 19875a8a45eb5e40a47fe177deafe690fb4f04fb"
author | nick |
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date | Tue, 31 Mar 2020 20:24:27 -0400 |
parents | 6cc488e11544 |
children | cf2af5c3118c |
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<tool id="allele_counts_1" version="1.3" name="Variant Annotator"> <description> process variant counts</description> <stdio> <exit_code range="1:" level="fatal" /> <exit_code range=":-1" level="fatal" /> </stdio> <command>allele-counts.py -i '$input' -o '$output' -f $freq -c $covg $header $stranded $nofilt #if $seed: -r '$seed' #end if </command> <inputs> <param name="input" type="data" format="vcf" label="Input variants from Naive Variants Detector"/> <param name="freq" type="float" value="1.0" min="0" max="100" label="Minor allele frequency threshold" help="in percent"/> <param name="covg" type="integer" value="10" min="0" label="Coverage threshold" help="in reads (per strand)"/> <param name="nofilt" type="boolean" truevalue="-n" falsevalue="" checked="False" label="Do not filter sites or alleles" /> <param name="stranded" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output stranded base counts" /> <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="True" label="Write header line" /> <param name="seed" type="text" value="" label="PRNG seed" /> </inputs> <outputs> <data name="output" format="tabular" /> </outputs> <tests> <test> <param name="input" value="tests/artificial.vcf.in" /> <param name="freq" value="10" /> <param name="covg" value="10" /> <param name="seed" value="1" /> <output name="output" file="tests/artificial.csv.out" /> </test> </tests> <help> .. class:: infomark **What it does** 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. ----- .. class:: infomark **Input Format** .. class:: warningmark **Note:** variants that are not A/C/G/T SNVs will be ignored! 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):: 0/0:1:0.02:+T=27,+G=1,-T=22, ----- .. class:: infomark **Output** Each row represents one site in one sample. For **unstranded** output, 13 fields give information about that site:: 1. SAMPLE - Sample name (from VCF sample column labels) 2. CHR - Chromosome of the site 3. POS - Chromosomal coordinate of the site 4. A - Number of reads supporting an 'A' 5. C - 'C' reads 6. G - 'G' reads 7. T - 'T' reads 8. CVRG - Total (number of reads supporting one of the four bases above) 9. ALLELES - Number of qualifying alleles 10. MAJOR - Major allele 11. MINOR - Minor allele (2nd most prevalent variant) 12. MAF - Frequency of minor allele 13. BIAS - Strand bias measure For stranded output, instead of using 4 columns to report read counts per base, 8 are used to report the stranded counts per base:: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 SAMPLE CHR POS +A +C +G +T -A -C -G -T CVRG ALLELES MAJOR MINOR MAF BIAS **Example** 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:: #SAMPLE CHR POS A C G T CVRG ALLELES MAJOR MINOR MAF BIAS BLOOD_1 chr20 99 0 101 1 2 104 1 C T 0.01923 0.33657 BLOOD_2 chr20 99 82 44 0 1 127 2 A C 0.34646 0.07823 BLOOD_3 chr20 99 0 110 1 0 111 1 C G 0.009 1.00909 BLOOD_1 chr20 100 3 5 100 0 108 1 G C 0.0463 0.15986 BLOOD_3 chr20 100 1 118 11 0 130 0 C G 0.08462 0.04154 ----- .. class:: warningmark **Site printing and allele tallying requirements** Coverage threshold: 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. Frequency threshold: If a frequency threshold is used, alleles are only counted (in the ALLELES column) if they meet or exceed this minor allele frequency threshold. Strand bias: 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. 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. </help> <citations> <citation type="bibtex"> @article{Blankenberg2014, 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}, doi = {10.1186/gb4161}, issn = {1465-6906}, journal = {Genome Biology}, keywords = {galaxy}, number = {2}, pages = {403}, title = {{Dissemination of scientific software with Galaxy ToolShed}}, url = {http://genomebiology.biomedcentral.com/articles/10.1186/gb4161}, volume = {15}, year = {2014} } </citation> <citation type="bibtex"> @article{Dickins2014, archivePrefix = {arXiv}, arxivId = {15334406}, 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}, doi = {10.2144/000114146}, eprint = {15334406}, isbn = {5049880467}, issn = {19409818}, journal = {BioTechniques}, number = {3}, pages = {134--141}, pmid = {24641477}, title = {{Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach}}, volume = {56}, year = {2014} } </citation> </citations> </tool>