Repository revision
9:f7ff063c738e

Repository 'annovar'
hg clone https://toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/annovar

ANNOVAR tool metadata
Miscellaneous
ANNOVAR
Annotate a file using ANNOVAR
AnnovarShed
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/annovar/AnnovarShed/2016march
2016march
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/annovar/AnnovarShed/2016march (this tool)
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/annovar/AnnovarShed/2015oct
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/annovar/AnnovarShed/2015may
toolshed.g2.bx.psu.edu/repos/saskia-hiltemann/annovar/AnnovarShed/2013aug
AnnovarShed
Requirements (dependencies defined in the <requirements> tag set)
name version type
cgatools 1.7 package
Additional information about this tool
annovar.sh
        --esp "${esp}"
        --gonl "${gonl}"
        --exac03 "${exac03}"
        --exac03nonpsych "${exac03nonpsych}"
        --exac03nontcga "${exac03nontcga}"
        --spidex "${spidex}"
        --gerp "${gerp}"
        --cosmic61 "${cosmic61}"
        --cosmic63 "${cosmic63}"
        --cosmic64 "${cosmic64}"
        --cosmic65 "${cosmic65}"
        --cosmic67 "${cosmic67}"
        --cosmic68 "${cosmic68}"
        --cosmic70 "${cosmic70}"
        --outall "${annotated}"
        --outinvalid "${invalid}"
        --dorunannovar "${dorun}"
        --inputfile "${infile}"
        --buildver "${reference.fields.dbkey}"
        --humandb "${reference.fields.ANNOVAR_humandb}"
        --scriptsdir "${reference.fields.ANNOVAR_scripts}"
        --verdbsnp "${verdbsnp}"
        --geneanno "${geneanno}"
        --tfbs "${tfbs}"
        --mce "${mce}"
        --cytoband "${cytoband}"
        --segdup "${segdup}"
        --dgv "${dgv}"
        --gwas "${gwas}"
        --dbscsnv11 "${dbscsnv11}"
        --kaviar_20150923 "${kaviar_20150923}"
        --hrcr1 "${hrcr1}"
        --mitimpact2 "${mitimpact2}"
        --mitimpact24 "${mitimpact24}"
        --dbnsfp30a "${dbnsfp30a}"
        #if $filetype.type == "other"
            --varfile N
            --VCF N
            --chrcol "${filetype.col_chr}"
            --startcol "${filetype.col_start}"
            --endcol "${filetype.col_end}"
            --obscol "${filetype.col_obs}"
            --refcol "${filetype.col_ref}"
            #if $filetype.convertcoords.convert == "Y"
                --vartypecol "${filetype.convertcoords.col_vartype}"
                --convertcoords Y
            #else
                --convertcoords N
            #end if
        #end if
        #if $filetype.type == "vcf"
            --varfile N
            --VCF Y
            --convertcoords N
        #end if
        #if $filetype.type == "varfile"
            --varfile Y
            --VCF N
        #end if
        --cg46 "${cgfortysix}"
        --cg69 "${cgsixtynine}"
        --ver1000g "${ver1000g}"
        --hgvs "${hgvs}"
        --otherinfo "${otherinfo}"
        --newimpactscores "${newimpactscores}"
        --clinvar "${clinvar}"
    
bash
False
False
Functional tests
No functional tests defined