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1 <tool id="vcfannotate" name="VCFannotate:" version="0.0.1">
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2 <requirements>
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3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
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4 </requirements>
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5 <description>Intersect VCF records with BED annotations</description>
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6 <command>vcfannotate --key "${key_option}" -b "${bed_data}" "${input}" > "${out_file1}"</command>
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7 <inputs>
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8 <param format="vcf" name="input" type="data" label="Select VCF dataset"/>
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9 <param name="bed_data" type="data" format="bed" label="BED datasets to itersect with"/>
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10 <param name="key_option" size="20" type="text" value="BED-features" label="Intersecting VCF records will be prefixed with this TAG within the INFO field" help="--key option"/>
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11 </inputs>
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12 <outputs>
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13 <data format="vcf" name="out_file1" />
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="bed_data" value="vcfannotate.bed" ftype="bed"/>
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18 <param name="key_option" value="BED-features"/>
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19 <param name="input" value="vcflib.vcf"/>
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20 <output name="out_file1" file="vcfannotate-test1.vcf" lines_diff="2" />
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21 </test>
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22 </tests>
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23 <help>
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24
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25 Intersect the records in the VCF file with targets provided in a BED file. Intersections are done on the reference sequences in the VCF file.
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26
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27 -----
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28
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29 .. class:: infomark
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30
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31
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32 **Example**:
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33
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34 The following VCF line::
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35
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36 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
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37 20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
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38
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39 will appear as the follwing after intersectuion with BED records uc010zpo.2, uc002wel.4, uc010zpp.2, and uc002wen::
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40
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41 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003
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42 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,.
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43
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44 ----
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45
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46 Vcfannotate is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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47
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48
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49 </help>
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50 </tool>
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