# HG changeset patch # User wolma # Date 1407928300 14400 # Node ID 995e258cc46c9b0092578ae40ba5072a67906916 Uploaded diff -r 000000000000 -r 995e258cc46c annotate_variants.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/annotate_variants.xml Wed Aug 13 07:11:40 2014 -0400 @@ -0,0 +1,164 @@ + + Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff + + mimodd + + + mimodd annotate + + $inputfile + + #if $str($annotool.name)=='snpeff': + --genome ${annotool.genomeVersion} + #if $annotool.ori_output: + --snpeff_out $snpeff_file + #end if + #if $annotool.stats: + --stats $summary_file + #end if + ${annotool.snpeff_settings.chr} ${annotool.snpeff_settings.no_us} ${annotool.snpeff_settings.no_ds} ${annotool.snpeff_settings.no_intron} ${annotool.snpeff_settings.no_intergenic} ${annotool.snpeff_settings.no_utr} + #if $annotool.snpeff_settings.min_cov: + --minC ${annotool.snpeff_settings.min_cov} + #end if + #if $annotool.snpeff_settings.min_qual: + --minQ ${annotool.snpeff_settings.min_qual} + #end if + #if $annotool.snpeff_settings.ud: + --ud ${annotool.snpeff_settings.ud} + #end if + #end if + + --ofile $outputfile + #if $str($formatting.oformat) == "text": + --oformat text + #end if + #if $str($formatting.oformat) == "html": + #if $formatting.formatter_file: + --link ${formatting.formatter_file} + #end if + #if $formatting.species + --species ${formatting.species} + #end if + #end if + + #if $str($grouping): + --grouping $grouping + #end if + --verbose + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ## default settings for SnpEff + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (annotool['name']=="snpeff" and annotool['ori_output']) + + + (annotool['name']=="snpeff" and annotool['stats']) + + + + +.. class:: infomark + + **What it does** + +The tool turns a variant list in VCF format into a more readable summary table listing variant sites and effects. + +If installed, the variant annotation tool SnpEff can be used transparently to determine the genomic features, e.g., genes or transcripts, affected by the variants. + +Use of this feature requires that you have an appropriate SnpEff genome file installed on the host machine. You can use the *List installed SnpEff genomes* tool to generate a list of all available SnpEff genomes. +This list can then be used (by selecting the dataset as the *genome list*) to populate the *genome* dropdown menu, from which you can select the SnpEff genome file to be used for the annotation. + +As output file formats HTML or plain text are supported. +In HTML mode, variant positions and/or affected genomic features can be turned into hyperlinks to corresponding views in web-based genome browsers. + +The behavior of this feature depends on: + +1) Recognition of the species that is analyzed + + You can declare the species you are working with using the *Species* text field. + If you are not declaring the species explicitly, but are choosing SnpEff for effect annotation, the tool will usually be able to auto-detect the species from the SnpEff genome you are using. + If no species gets assigned in either way, no hyperlinks will be generated and the html output will look essentially like plain text. + +2) Available hyperlink formatting rules for this species + + When the species has been recognized, the tool checks if you have selected an *optional file with hyperlink formatting instructions*. + If you did and that file contains an entry matching the recognized species, that entry will be used as a template to construct the hyperlinks. + If no matching entry is found in the file, an error will be raised. + + If you did not supply a hyperlink formatting instruction file, the tool will consult an internal lookup table to see if it finds default rules for the construction of the hyperlinks for the species. + If not, no hyperlinks will be generated and the html output will look essentially like plain text. + + + +