Mercurial > repos > iuc > snpeff
changeset 7:7adfd0589f49 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 5c6d595ecbf2e4e39c25662a165c9e475e01ecd1
| author | iuc |
|---|---|
| date | Tue, 18 Apr 2017 09:33:56 -0400 |
| parents | 20f0429a4bfe |
| children | ce135864629c |
| files | readme.rst snpEff.xml snpEff_databases.xml snpEff_download.xml snpEff_macros.xml test-data/input.vcf test-data/vcf_homhet.vcf tool_dependencies.xml |
| diffstat | 8 files changed, 171 insertions(+), 266 deletions(-) [+] |
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--- a/readme.rst Mon Dec 19 11:56:53 2016 -0500 +++ b/readme.rst Tue Apr 18 09:33:56 2017 -0400 @@ -6,14 +6,6 @@ .. _SnpEff: http://snpeff.sourceforge.net/ - -This repository let you automatically install SnpEff and SnpSift. -This will use the default location for genome reference downloads from the ``snpEff.config`` file: - - data_dir = ~/snpEff/data/ - -You can manually edit the installed ``snpEff.config`` file and change the location, or you can create a symbolic link to the desired data location from ``~/snpEff``. - The genome reference options used by the tools "SnpEff" (snpEff.xml) and "SnpEff Download" (snpEff_download.xml) are taken from the ``tool-data/snpeffect_genomedb.loc`` file. You can fill this file by running the following command: @@ -35,4 +27,3 @@ .. _Cingolani2012using: http://journal.frontiersin.org/Journal/10.3389/fgene.2012.00035/ Wrapper authors: Jim Johnson -
--- a/snpEff.xml Mon Dec 19 11:56:53 2016 -0500 +++ b/snpEff.xml Tue Apr 18 09:33:56 2017 -0400 @@ -6,23 +6,20 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> -<![CDATA[ - @CONDA_SNPEFF_JAR_PATH@ && - java -Xmx6G -jar "\$SNPEFF_JAR_PATH/snpEff.jar" eff - -c "\$SNPEFF_JAR_PATH/snpEff.config" + <command><![CDATA[ + snpEff -Xmx8g eff -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength #if $spliceSiteSize and str($spliceSiteSize) != '': -spliceSiteSize "$spliceSiteSize" #end if #if $spliceRegion.setSpliceRegions == 'yes': - #if $spliceRegion.spliceRegionExonSize and str($spliceRegion.spliceRegionExonSize) != '': + #if str($spliceRegion.spliceRegionExonSize) -spliceRegionExonSize $spliceRegion.spliceRegionExonSize #end if - #if $spliceRegion.spliceRegionIntronMin and str($spliceRegion.spliceRegionIntronMin) != '': + #if str($spliceRegion.spliceRegionIntronMin) -spliceRegionIntronMin $spliceRegion.spliceRegionIntronMin #end if - #if $spliceRegion.spliceRegionIntronMax and str($spliceRegion.spliceRegionIntronMax) != '': + #if str($spliceRegion.spliceRegionIntronMax) -spliceRegionIntronMax $spliceRegion.spliceRegionIntronMax #end if #end if @@ -39,63 +36,63 @@ -no $eff #end for #end if - #if str( $transcripts ) != 'None': - -onlyTr $transcripts + #if $transcripts + -onlyTr '$transcripts' #end if - #if str( $intervals ) != 'None': ### fix this for multiple dataset input - -interval $intervals + #if $intervals ### fix this for multiple dataset input + -interval '$intervals' #end if #if $statsFile: - -stats $statsFile + -stats '$statsFile' #end if #if str($offset) != 'default': ${offset} #end if #if str($chr).strip() != '': - -chr "$chr" + -chr '$chr' #end if $noLog + ## Regulation names can include parentheses: H3K4me3-MSC_(VB)_enriched_sites + ## Enclose them in in single and double quotes, as the conda snpEff bash script will remove outer quotes #if $snpDb.genomeSrc == 'cached': -dataDir ${snpDb.genomeVersion.fields.path} - #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '': - #echo " " - #echo ' '.join(str($snpDb.extra_annotations).split(',')) - #end if - #if $snpDb.regulation and str($snpDb.regulation) != '': - -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))# + #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '': + #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')] + #for reg in $regs: + -reg '"${reg}"' + #end for #end if $snpDb.genomeVersion #elif $snpDb.genomeSrc == 'history': - -dataDir ${snpDb.snpeff_db.extra_files_path} - #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != '': - #set xannotations = [' '] + str($snpDb.extra_annotations).split(',') - #echo " " - #echo ' -'.join($xannotations) + -dataDir '${snpDb.snpeff_db.extra_files_path}' + #if $snpDb.reg_section.regulation and str($snpDb.reg_section.regulation) != '': + #set $regs = [x for x in str($snpDb.reg_section.regulation).split(',')] + #for reg in $regs: + -reg '"${reg}"' + #end for #end if - #if $snpDb.regulation and str($snpDb.regulation) != '': - -reg #echo ' -reg '.join(str($snpDb.regulation).split(','))# - #end if - ${snpDb.snpeff_db.metadata.genome_version} + '${snpDb.snpeff_db.metadata.genome_version}' #else -download - $snpDb.genome_version + '$snpDb.genome_version' #end if - "$input" > "$snpeff_output"; + '$input' > '$snpeff_output' #if $statsFile: + && #import os #set $genes_file = str($statsFile) + '.genes.txt' #set $genes_file_name = os.path.split($genes_file)[-1] - mkdir $statsFile.files_path; - mv "$genes_file" #echo os.path.join($statsFile.files_path, $genes_file_name)#; + mkdir '$statsFile.files_path' && + mv '$genes_file' '#echo os.path.join($statsFile.files_path, $genes_file_name)#' #end if #if $outputConditional.outputFormat == 'gatk' and $outputConditional.gatk_v1 + && ## Replace real SnpEff version with 2.0.5 to prevent this GATK 1.x error: "The version of SnpEff used to generate the SnpEff input file (x.x) is not currently supported by the GATK. Supported versions are: [2.0.5]" - sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' "$snpeff_output" + sed -i.bak -e 's/^\#\#SnpEffVersion="\(\S*\s\)/\#\#SnpEffVersion="2.0.5 - real is \1/' '$snpeff_output' #end if -]]> - </command> + ]]></command> <inputs> - <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> + <param name="input" type="data" format="vcf,tabular,pileup,bed" label="Sequence changes (SNPs, MNPs, InDels)"/> <param name="inputFormat" type="select" label="Input format"> <option value="vcf" selected="true">VCF</option> @@ -127,45 +124,34 @@ <param name="genomeVersion" type="select" label="Genome"> <!--GENOME DESCRIPTION--> <options from_data_table="snpeffv_genomedb"> - <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/> - <filter type="unique_value" column="2" /> + <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/> + <filter type="unique_value" column="2" /> </options> </param> - <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> - <help>These are available for only a few genomes</help> - <options from_data_table="snpeffv_annotations"> - <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> - <filter type="unique_value" column="3" /> - </options> - </param> - <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> - <help>These are available for only a few genomes</help> - <options from_data_table="snpeffv_regulationdb"> - <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> - <filter type="unique_value" column="3" /> - </options> - </param> + <section name="reg_section" expanded="false" title="Regulation options"> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes"> + <options from_data_table="snpeffv_regulationdb"> + <filter type="param_value" ref="genomeVersion" key="genome" column="2" /> + <filter type="unique_value" column="3" /> + </options> + </param> + </section> </when> <when value="history"> - <param format="snpeffdb" name="snpeff_db" type="data" label="@SNPEFF_VERSION@ Genome Data"> + <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data"> <options options_filter_attribute="metadata.snpeff_version" > <filter type="add_value" value="@SNPEFF_VERSION@" /> </options> - <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ Genome databases.">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> + <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator> </param> - <!-- From metadata --> - <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> - <help>These are available for only a few genomes</help> - <options> - <filter type="data_meta" ref="snpeff_db" key="annotation" /> - </options> - </param> - <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation"> - <help>These are available for only a few genomes</help> - <options> - <filter type="data_meta" ref="snpeff_db" key="regulation" /> - </options> - </param> + <section name="reg_section" expanded="false" title="Regulation options"> + <!-- From metadata --> + <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes"> + <options> + <filter type="data_meta" ref="snpeff_db" key="regulation" /> + </options> + </param> + </section> </when> <when value="named"> <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> @@ -186,7 +172,7 @@ <option value="20000">20000 bases</option> </param> - <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases" help="Default: 2"> + <param name="spliceSiteSize" type="select" optional="true" label="Set size for splice sites (donor and acceptor) in bases"> <option value="1">1 base</option> <option value="2" selected="true">2 bases</option> <option value="3">3 bases</option> @@ -212,24 +198,33 @@ </conditional> <param name="annotations" type="select" display="checkboxes" multiple="true" label="Annotation options"> - <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> - <option value="-canon">Only use canonical transcripts</option> - <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> - <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option> - <option value="-oicr">Add OICR tag in VCF file</option> - <option value="-onlyReg">Only use regulation tracks</option> + <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN')</option> <option value="-classic">Use Classic Effect names and amino acid variant annotations (NON_SYNONYMOUS_CODING vs missense_variant and G180R vs p.Gly180Arg/c.538G>C)</option> + <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> <option value="-hgvs">Override classic and use HGVS annotations for amino acid annotations (p.Gly180Arg/c.538G>C vs G180R)</option> - <option value="-sequenceOntology">Override classic and use Sequence Ontolgy terms for effects (missense_variant vs NON_SYNONYMOUS_CODING)</option> - <option value="-formatEff">Use 'EFF' field compatible with older versions (instead of 'ANN').</option> - <option value="-noHgvs">Do not add HGVS annotations.</option> - <option value="-noLof">Do not add LOF and NMD annotations.</option> - <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end).</option> - <option value="-oicr">Add OICR tag in VCF file. Default: false</option> + <option value="-hgvsOld">Old notation style notation: E.g. 'c.G123T' instead of 'c.123G>T' and 'X' instead of '*'</option> + <option value="-hgvs1LetterAa">Use one letter Amino acid codes in HGVS notation. E.g. p.R47G instead of p.Arg47Gly</option> + <option value="-hgvsTrId">Use transcript ID in HGVS notation. E.g. ENST00000252100:c.914C>G instead of c.914C>G</option> + <option value="-noShiftHgvs">Do not shift variants according to HGVS notation (most 3prime end)</option> + <option value="-noHgvs">Do not add HGVS annotations</option> + <option value="-canon">Only use canonical transcripts</option> + <option value="-onlyProtein">Only use protein coding transcripts</option> + <option value="-geneId">Use gene ID instead of gene name (VCF output)</option> + <option value="-noExpandIUB">Disable IUB code expansion in input variants</option> + <option value="-oicr">Add OICR tag in VCF file</option> + <option value="-lof">Add loss of function (LOF) and nonsense mediated decay (NMD) tags</option> + <option value="-noLof">Do not add LOF and NMD annotations</option> + <option value="-noMotif">Disable motif annotations</option> + <option value="-noNextProt">Disable NextProt annotations</option> + <option value="-noInteraction">Disable interaction annotations</option> + <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> + <!-- onlyReg option results in ifrequent exceptions with version 4.3k + <option value="-onlyReg">Only use regulation tracks</option> + --> </param> <!-- -cancerSamples <file> : Two column TXT file defining 'oringinal \t derived' samples. --> - <param name="intervals" format="bed" type="data" optional="true" label="Use custom interval file for annotation"/> - <param name="transcripts" format="tabular" type="data" optional="true" label="Only use the transcripts in this file." help="Format is one transcript ID per line."/> + <param name="intervals" type="data" format="bed" optional="true" label="Use custom interval file for annotation"/> + <param name="transcripts" type="data" format="tabular" optional="true" label="Only use the transcripts in this file" help="Format is one transcript ID per line"/> <param name="filterOut" type="select" display="checkboxes" multiple="true" label="Filter output"> <option value="-no-downstream">Do not show DOWNSTREAM changes</option> <option value="-no-intergenic">Do not show INTERGENIC changes</option> @@ -287,12 +282,11 @@ <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5'UTR region MODIFIER</option> <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5'UTR of the transcript MODERATE</option> <option value="NEXT_PROT">NEXT_PROT (sequence_feature + exon_loss_variant) A 'NextProt' based annotation. Details are provided in the 'feature type' sub-field (ANN), or in the effect details (EFF). MODERATE </option> - </param> </when> </conditional> - <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> + <param name="offset" type="select" display="radio" label="Chromosomal position"> <option value="default" selected="true">Use default (based on input type)</option> <option value="-0">Force zero-based positions (both input and output)</option> <option value="-1">Force one-based positions (both input and output)</option> @@ -300,7 +294,7 @@ <param name="chr" type="text" label="Text to prepend to chromosome name"> <help> By default SnpEff simplifies all chromosome names. For instance 'chr1' is just '1'. - You can prepend any string you want to the chromosome name. + You can prepend any string you want to the chromosome name </help> <validator type="regex" message="No whitespace allowed">^\S*$</validator> </param> @@ -308,93 +302,38 @@ <param name="noLog" type="boolean" truevalue="-noLog" falsevalue="" checked="true" label="Suppress reporting usage statistics to server"/> </inputs> <outputs> - <data format="vcf" name="snpeff_output" > + <data name="snpeff_output" format="vcf"> <change_format> <when input="outputConditional.outputFormat" value="bed" format="bed" /> <when input="outputConditional.outputFormat" value="bedAnn" format="bed" /> </change_format> </data> - <data format="html" name="statsFile" label="${tool.name} on ${on_string} - stats"> + <data name="statsFile" format="html" label="${tool.name} on ${on_string} - stats"> <filter>generate_stats == True</filter> </data> </outputs> <tests> - <!-- Check that an effect was added in out VCF --> - <!-- Check for a HTML header indicating that this was successful --> - <!-- - <output name="statsFile"> - <assert_contents> - <has_text text="SnpEff: Variant analysis" /> - </assert_contents> - </output> - --> - <!-- Setting filterOut throws exception in twilltestcase.py <test> - <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> - <param name="inputFormat" value="vcf"/> - <param name="outputFormat" value="vcf"/> - <param name="genomeSrc" value="named"/> - <param name="genome_version" value="testCase"/> - <param name="udLength" value="0"/> - <param name="generate_stats" value="False"/> - <param name="filterOut" value="+-no-upstream"/> - <output name="snpeff_output"> - <assert_contents> - <has_text text="EFF=" /> - </assert_contents> - </output> + <param name="input" ftype="vcf" value="input.vcf"/> + <param name="inputFormat" value="vcf"/> + <param name="outputFormat" value="vcf"/> + <param name="genomeSrc" value="named"/> + <param name="genome_version" value="ebola_zaire"/> + <param name="udLength" value="0"/> + <param name="generate_stats" value="False"/> + <output name="snpeff_output"> + <assert_contents> + <has_text_matching expression="KJ660346\t572\t.*missense_variant" /> + <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" /> + </assert_contents> + </output> </test> - --> - - <test> - <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> - <param name="inputFormat" value="vcf"/> - <param name="outputFormat" value="vcf"/> - <param name="genomeSrc" value="named"/> - <param name="genome_version" value="testCase"/> - <param name="udLength" value="0"/> - <!-- - <param name="filterOut" value=""/> - --> - <param name="generate_stats" value="False"/> - <output name="snpeff_output"> - <assert_contents> - <!-- Check that deleletions were evaluated --> - <has_text_matching expression="Y\t59030478\t.*intergenic_region" /> - <!-- Check that insertion on last line was NOT evaluated --> - <has_text_matching expression="Y\t59032947\t.*\tGT" /> - </assert_contents> - </output> - </test> - - <!-- Check that NO UPSTREAM effect was added --> - <!-- Setting filterOut throws exception in twilltestcase.py - <test> - <param name="input" ftype="vcf" value="vcf_homhet.vcf"/> - <param name="inputFormat" value="vcf"/> - <param name="outputFormat" value="vcf"/> - <param name="genomeSrc" value="named"/> - <param name="genome_version" value="testCase"/> - <param name="udLength" value="0"/> - <param name="filterOut" value="+-no-upstream"/> - <param name="generate_stats" value="False"/> - <output name="snpeff_output"> - <assert_contents> - <not_has_text text="UPSTREAM" /> - </assert_contents> - </output> - </test> - --> - </tests> <help><![CDATA[ - This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. @EXTERNAL_DOCUMENTATION@ - ]]> </help> <expand macro="citations" /> </tool> -
--- a/snpEff_databases.xml Mon Dec 19 11:56:53 2016 -0500 +++ b/snpEff_databases.xml Tue Apr 18 09:33:56 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0"> +<tool id="snpEff_databases" name="SnpEff available databases" version="@WRAPPER_VERSION@.0"> <description></description> <macros> <import>snpEff_macros.xml</import> @@ -6,12 +6,9 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> -<![CDATA[ - @CONDA_SNPEFF_JAR_PATH@ && - java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > "$snpeff_dbs" -]]> - </command> + <command><![CDATA[ +snpEff databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > '$snpeff_dbs' + ]]></command> <inputs> </inputs> <outputs> @@ -27,11 +24,8 @@ </test> </tests> <help><![CDATA[ - @EXTERNAL_DOCUMENTATION@ - -]]> - </help> + ]]></help> <expand macro="citations" /> </tool>
--- a/snpEff_download.xml Mon Dec 19 11:56:53 2016 -0500 +++ b/snpEff_download.xml Tue Apr 18 09:33:56 2017 -0400 @@ -6,14 +6,11 @@ <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> - <command> -<![CDATA[ - @CONDA_SNPEFF_JAR_PATH@ && - java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" download -c "\$SNPEFF_JAR_PATH/snpEff.config" -dataDir "$snpeff_db.files_path" -v "$genome_version" -]]> - </command> + <command><![CDATA[ +snpEff download -dataDir '$snpeff_db.files_path' -v '$genome_version' + ]]></command> <inputs> - <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh37.74)"> + <param name="genome_version" type="text" value="" label="Select the genome version you want to download (e.g. GRCh38.86, GRCh37.75, hg38, or GRCm38.86)"> <help>@SNPEFF_DATABASE_URL@</help> <validator type="regex" message="A genome version name is required">\S+</validator> </param> @@ -32,11 +29,7 @@ </test> </tests> <help><![CDATA[ - @EXTERNAL_DOCUMENTATION@ - -]]> - </help> + ]]></help> <expand macro="citations" /> </tool> -
--- a/snpEff_macros.xml Mon Dec 19 11:56:53 2016 -0500 +++ b/snpEff_macros.xml Tue Apr 18 09:33:56 2017 -0400 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.1">snpEff</requirement> + <requirement type="package" version="4.3k">snpeff</requirement> </requirements> </xml> <xml name="stdio"> @@ -10,22 +10,16 @@ <exit_code range="1:" level="fatal" description="Error" /> </stdio> </xml> - <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token> <xml name="version_command"> <version_command><![CDATA[ - if [ -z "$SNPEFF_JAR_PATH" ]; then - export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff))); - fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version +snpEff -version ]]></version_command> </xml> - <token name="@WRAPPER_VERSION@">4.1</token> - <token name="@SNPEFF_VERSION@">SnpEff4.1</token> - <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token> + <token name="@WRAPPER_VERSION@">4.3k</token> + <token name="@SNPEFF_VERSION@">SnpEff4.3</token> + <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token> <token name="@EXTERNAL_DOCUMENTATION@"> - -For details about this tool, please go to: - http://snpeff.sourceforge.net/SnpEff_manual.html - +For details about this tool, please go to: http://snpeff.sourceforge.net/SnpEff_manual.html </token> <xml name="citations"> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.vcf Tue Apr 18 09:33:56 2017 -0400 @@ -0,0 +1,60 @@ +##fileformat=VCFv4.1 +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##contig=<ID="KJ660346",length=18959> +##reference=http://www.ncbi.nlm.nih.gov/nuccore/KJ660346.2 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT EBOV_2014_EM095 EBOV_2014_G3676 EBOV_2014_G3680 EBOV_2014_G3686 EBOV_2014_G3687 EBOV_2014_G3683 EBOV_2014_EM096 EBOV_2014_EM098 EBOV_2014_EM104 EBOV_2014_EM106 EBOV_2014_EM112 EBOV_2014_EM113 EBOV_2014_EM124 EBOV_2014_G3677 EBOV_2014_G3682 EBOV_2014_G3707 EBOV_2014_G3713 EBOV_2014_G3724 EBOV_2014_G3734 EBOV_2014_G3735 EBOV_2014_G3750 EBOV_2014_G3758 EBOV_2014_G3764 EBOV_2014_G3769 EBOV_2014_G3782 EBOV_2014_G3786 EBOV_2014_G3788 EBOV_2014_G3796 EBOV_2014_G3798 EBOV_2014_G3799 EBOV_2014_G3800 EBOV_2014_G3805 EBOV_2014_G3807 EBOV_2014_G3810 EBOV_2014_G3820 EBOV_2014_G3838 EBOV_2014_G3840 EBOV_2014_G3841 EBOV_2014_G3848 EBOV_2014_NM042 EBOV_2014_G3850 EBOV_2014_EM110 EBOV_2014_EM111 EBOV_2014_EM119 EBOV_2014_G3729 EBOV_2014_G3765 EBOV_2014_G3770 EBOV_2014_G3789 EBOV_2014_G3825 EBOV_2014_G3845 EBOV_2014_G3851 EBOV_2014_G3857 EBOV_2014_EM115 EBOV_2014_EM120 EBOV_2014_G3752 EBOV_2014_G3795 EBOV_2014_G3808 EBOV_2014_G3823 EBOV_2014_EM121 EBOV_2014_G3771 EBOV_2014_G3816 EBOV_2014_G3829 EBOV_2014_G3846 EBOV_2014_G3856 EBOV_2014_G3826 EBOV_2014_G3827 EBOV_2014_G3809 EBOV_2014_G3814 EBOV_2014_G3821 EBOV_2014_G3822 EBOV_2014_G3679 EBOV_2014_G3819 EBOV_2014_G3817 EBOV_2014_G3834 EBOV_2014_G3818 EBOV_2014_G3787 EBOV_2014_G3831 EBOV_2014_G3670 EBOV_2014_KJ660346 EBOV_2014_KJ660347 EBOV_2014_KJ660348 +KJ660346 572 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 800 . C T . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 +KJ660346 1024 . A C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 1288 . A T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 +KJ660346 1492 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 1849 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 +KJ660346 2124 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +KJ660346 2185 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +KJ660346 2341 . A G . . . GT 0 0 0 0 . 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 +KJ660346 2364 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 2497 . A G . . . GT 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 2931 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 +KJ660346 3116 . C G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 3388 . T G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +KJ660346 3638 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 +KJ660346 4340 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +KJ660346 4505 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 4709 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 4759 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 4976 . C A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 5461 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 6175 . G A . . . GT 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 6283 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 +KJ660346 6909 . T A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 +KJ660346 8280 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 +KJ660346 8928 . A C . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 +KJ660346 9390 . A C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 9536 . A G . . . GT 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 9923 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 +KJ660346 10005 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 +KJ660346 10218 . G A . . . GT 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 1 1 1 0 1 1 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 1 0 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 0 1 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 0 0 0 0 0 0 +KJ660346 10252 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 +KJ660346 10268 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 10509 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 10743 . T C . . . GT 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 10801 . A G . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 11142 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 11811 . T C . . . GT 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +KJ660346 11943 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 +KJ660346 12878 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 12885 . A C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . . . +KJ660346 13856 . G A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 +KJ660346 13923 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 +KJ660346 14019 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 1 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 +KJ660346 14232 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 15599 . G A . . . GT 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +KJ660346 15660 . C T . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 +KJ660346 15963 . G A . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 +KJ660346 16054 . T A . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 +KJ660346 16455 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 +KJ660346 16750 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 17142 . T C . . . GT 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 +KJ660346 17985 . T C . . . GT 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +KJ660346 18412 . T C . . . GT 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 +KJ660346 18895 . C T . . . GT 0 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 . 0 0 0 0 . 0 . 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 . 0 0 0 0 0 0 0 0 0 0 0 1 1 1
--- a/test-data/vcf_homhet.vcf Mon Dec 19 11:56:53 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,60 +0,0 @@ -##fileformat=VCFv4.0 -##samtoolsVersion=0.1.15 (r949:203) -##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> -##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> -##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads"> -##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> -##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele"> -##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> -##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> -##INFO=<ID=CI95,Number=2,Type=Float,Description="Equal-tail Bayesian credible interval of the site allele frequency at the 95% level"> -##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> -##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> -##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> -##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> -##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> -##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> -##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> -##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> -##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases"> -##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> -##FORMAT=<ID=PL,Number=.,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2"> -##source_20110319.1=/wsu/home/eq/eq83/eq8302/tools/vcftools/bin//vcf-merge s_1_ACAGTGA.vcf.gz s_1_CAGATCA.vcf.gz s_1_CGATGTA.vcf.gz s_1_CTTGTAA.vcf.gz s_1_GCCAATA.vcf.gz s_1_TGACCAA.vcf.gz -##sourceFiles_20110319.1=0:s_1_ACAGTGA.vcf.gz,1:s_1_CAGATCA.vcf.gz,2:s_1_CGATGTA.vcf.gz,3:s_1_CTTGTAA.vcf.gz,4:s_1_GCCAATA.vcf.gz,5:s_1_TGACCAA.vcf.gz -##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)"> -##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT s_1_ACAGTGA_sort.bam s_1_CAGATCA_sort.bam s_1_CGATGTA_sort.bam s_1_CTTGTAA_sort.bam s_1_GCCAATA_sort.bam s_1_TGACCAA_sort.bam -Y 3718196 . C T 7.59 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=4.617e-16,8.575e-07,1;MQ=39;SF=1 GT:GQ:PL . 1/1:61:38,6,0 . . . . -Y 3720217 . A G 8.65 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=2;FQ=-30;G3=4.415e-15,5.291e-06,1;MQ=38;SF=5 GT:GQ:PL . . . . . 1/1:53:38,3,0 -Y 3720581 . A G 7.80 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-30;G3=5.56e-15,5.291e-06,1;MQ=44;SF=1 GT:GQ:PL . 1/1:53:37,3,0 . . . . -Y 3721154 . A G 13.90 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=9.194e-17,8.566e-07,1;MQ=37;SF=3 GT:GQ:PL . . . 1/1:61:45,6,0 . . -Y 3721230 . C G 21.80 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.456e-17,8.564e-07,1;MQ=29;SF=3 GT:GQ:PL . . . 1/1:61:53,6,0 . . -Y 3744605 . C A 3.98 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-33;G3=1.468e-15,8.599e-07,1;MQ=19;SF=2 GT:GQ:PL . . 1/1:61:33,6,0 . . . -Y 4433091 . T C 11.10 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-33;G3=1.835e-16,8.568e-07,1;MQ=23;SF=5 GT:GQ:PL . . . . . 1/1:61:42,6,0 -Y 9945223 . ATTT ATTTT 19.80 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=2.906e-18,8.564e-07,1;INDEL;MQ=45;SF=0,2 GT:GQ:PL 1/1:61:60,6,0 . 1/1:61:57,6,0 . . . -Y 9987395 . TTAT TT 80.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,1,2;DP=3;FQ=-43.5;G3=5.464e-26,5.886e-08,1;INDEL;MQ=43;SF=5 GT:GQ:PL . . . . . 1/1:72:120,9,0 -Y 10011604 . C CTT 119.17 . AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,7,0;DP=9;FQ=-55.5;G3=4.948e-32,3.15e-11,1;INDEL;MQ=33;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:99:139,21,0 1/1:96:134,24,0 1/1:99:168,36,0 1/1:99:159,45,0 1/1:99:185,33,0 1/1:99:175,39,0 -Y 10011748 . GAAAAAA GAAAAAAA 23.70 . AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=12,12,11,10;DP=51;FQ=33.5;G3=1.256e-14,1,1.991e-19;INDEL;MQ=33;PV4=1,0.49,0.012,0.2;SF=0,1,2,3,4,5 GT:GQ:PL 0/0:71:68,0,92 1/1:55:52,0,77 1/1:71:69,0,75 1/1:69:66,0,79 1/1:56:53,0,80 1/1:62:59,0,98 -Y 10011894 . ATTATTTATTT ATTATTT 58.62 . AC=4;AF1=0.5;AN=8;CI95=0.5,0.5;DP4=4,11,0,6;DP=34;FQ=32.5;G3=1.991e-14,1,7.924e-52;INDEL;MQ=35;PV4=0.28,0.049,0.14,0.2;SF=1,3,4,5 GT:GQ:PL . 0/0:70:67,0,254 . 1/1:99:152,0,255 1/1:83:80,0,255 1/1:89:86,0,255 -Y 10011930 . ACT A 90.85 . AC=2;AF1=0.5;AN=4;CI95=0.5,0.5;DP4=2,6,1,3;DP=17;FQ=16.6;G3=3.155e-11,1,1.991e-34;INDEL;MQ=35;PV4=1,0.00044,0.33,1;SF=0,5 GT:GQ:PL 0/0:54:51,0,167 . . . . 0/0:99:206,0,255 -Y 10011935 . C CT 83.83 . AC=3;AF1=0.5;AN=6;CI95=0.5,0.5;DP4=1,8,2,5;DP=23;FQ=90.3;G3=1.256e-28,1,5e-26;INDEL;MQ=39;PV4=0.55,1,0.15,1;SF=1,2,4 GT:GQ:PL . 0/0:99:138,0,125 1/1:92:89,0,148 . 1/1:99:138,0,171 . -Y 10011966 . ATT AT 79.38 . AC=6;AF1=0.5;AN=12;CI95=0.5,0.5;DP4=1,6,0,2;DP=14;FQ=5.09;G3=1.991e-12,1,1.256e-28;INDEL;MQ=38;PV4=1,1,0.46,0.088;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:41:38,0,92 1/1:76:73,0,109 1/1:99:181,0,109 1/1:99:114,0,103 1/1:99:139,0,171 1/1:99:155,0,144 -Y 10028061 . CA CAA 28.40 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,2,1;DP=9;FQ=-43.5;G3=2.739e-22,5.886e-08,1;INDEL;MQ=37;SF=4,5 GT:GQ:PL . . . . 1/1:72:83,9,0 0/0:61:52,6,0 -Y 10029194 . CA C 73.47 . AC=10;AF1=0.7304;AN=12;CI95=0.5,1;DP4=2,0,7,3;DP=19;FQ=-32.5;G3=2.922e-150,0.9991,0.000854;INDEL;MQ=25;PV4=1,0.4,1,0.23;SF=0,1,2,3,4,5 GT:GQ:PL 0/0:3:93,0,2 1/1:85:100,17,0 1/1:99:181,36,0 1/1:90:107,18,0 1/1:3:104,0,2 1/1:70:90,10,0 -Y 10029452 . CAA CAAA 7.26 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,4,0;DP=13;FQ=-46.5;G3=2.341e-18,6.106e-08,1;INDEL;MQ=26;SF=3,4 GT:GQ:PL . . . 1/1:72:50,12,0 1/1:72:42,12,0 . -Y 10037877 . GCCC GCCCC 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=3;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2 GT:GQ:PL . . 1/1:61:53,6,0 . . . -Y 13266272 . TTTT TTTTATTT 51.50 . AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=5,1,7,0;DP=15;FQ=54.5;G3=7.924e-19,1,3.155e-24;INDEL;MQ=30;PV4=0.46,1,0.078,0.00035;SF=3 GT:GQ:PL . . . 0/0:92:89,0,116 . . -Y 13268110 . GC GCC 3.66 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.911e-16,8.571e-07,1;INDEL;MQ=23;SF=2 GT:GQ:PL . . 1/1:61:40,6,0 . . . -Y 13292082 . TCCCCCCCCCC TCCCCCCC 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=3 GT:GQ:PL . . . 1/1:61:53,6,0 . . -Y 13297070 . AGGTGGTGGTGGT AGGTGGTGGT 12.70 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,1;DP=1;FQ=-37.5;G3=2.782e-16,5.287e-06,1;INDEL;MQ=50;SF=5 GT:GQ:PL . . . . . 1/1:53:50,3,0 -Y 13312198 . CGGGGG CGGGG 14.87 . AC=5;AF1=1;AN=6;CI95=0.5,1;DP4=2,0,10,0;DP=12;FQ=-43.5;G3=1.373e-19,5.886e-08,1;INDEL;MQ=24;PV4=1,0.44,1,0.019;SF=1,4,5 GT:GQ:PL . 1/1:72:56,9,0 . . 1/1:70:57,10,0 1/1:44:48,0,42 -Y 13312608 . CA CAA 22.50 . AC=1;AF1=0.5032;AN=2;CI95=0.5,0.5;DP4=2,0,7,0;DP=16;FQ=-15.6;G3=4.937e-25,1,1.272e-08;INDEL;MQ=24;PV4=1,1,0.093,1;SF=2 GT:GQ:PL . . 0/0:22:60,0,19 . . . -Y 13402810 . TAGAGA TAGA 29.80 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,1;DP=2;FQ=-40.5;G3=7.299e-19,8.564e-07,1;INDEL;MQ=33;SF=0,2 GT:GQ:PL 1/1:61:66,6,0 . 1/1:72:72,9,0 . . . -Y 21153016 . AG ATG 213.83 . AC=12;AF1=1;AN=12;CI95=1,1;DP4=0,0,6,9;DP=15;FQ=-79.5;G3=7.905e-54,1e-18,1;INDEL;MQ=43;SF=0,1,2,3,4,5 GT:GQ:PL 1/1:99:255,45,0 1/1:99:.,.,0 1/1:99:255,87,0 1/1:99:.,.,0 1/1:99:255,78,0 1/1:99:.,.,0 -Y 21153067 . CCA C 46.50 . AC=1;AF1=0.5;AN=2;CI95=0.5,0.5;DP4=8,4,5,0;DP=18;FQ=49.5;G3=7.924e-18,1,5e-52;INDEL;MQ=39;PV4=0.26,0.08,0.035,1;SF=3 GT:GQ:PL . . . 0/0:87:84,0,255 . . -Y 26325233 . TGAGAGAGAGAGA TGAGAGAGAGA 22.20 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,2,0;DP=2;FQ=-40.5;G3=2.308e-18,8.564e-07,1;INDEL;MQ=33;SF=0 GT:GQ:PL 1/1:61:61,6,0 . . . . . -Y 28588049 . ACATCAT ACAT 7.35 . AC=4;AF1=1;AN=4;CI95=0.5,1;DP4=0,0,1,0;DP=1;FQ=-37.5;G3=1.108e-15,5.288e-06,1;INDEL;MQ=44;SF=1,3 GT:GQ:PL . 1/1:53:44,3,0 . 1/1:53:44,3,0 . . -Y 59030478 . AAAACAAACAAACAAACAAACAAACAAA AAAACAAACAAACAAA 14.40 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=1.456e-17,8.564e-07,1;INDEL;MQ=29;SF=2 GT:GQ:PL . . 1/1:61:53,6,0 . . . -Y 59032947 . GTT GTTT 28.20 . AC=2;AF1=1;AN=2;CI95=0.5,1;DP4=0,0,0,2;DP=2;FQ=-40.5;G3=5.798e-19,8.564e-07,1;INDEL;MQ=37;SF=5 GT:GQ:PL . . . . . 1/1:61:67,6,0
--- a/tool_dependencies.xml Mon Dec 19 11:56:53 2016 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="snpEff" version="4.1"> - <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>