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1 <tool id="vcffilter" name="VCFfilter:" 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>filter VCF data in a variety of attributes</description>
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6 <command>vcffilter ${filterList} "${input}" > "${out_file1}"</command>
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7 <inputs>
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8 <param name="filterList" size="40" type="text" value="-f "DP > 10"" label="Specify filterting expression" help="See explanation of filtering options below">
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9 <sanitizer>
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10 <valid initial="string.printable">
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11 <remove value="'"/>
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12 </valid>
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13 <mapping initial="none">
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14 <add source="'" target="__sq__"/>
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15 </mapping>
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16 </sanitizer>
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17 </param>
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18 <param format="vcf" name="input" type="data" label="From"/>
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19 </inputs>
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20 <outputs>
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21 <data format="vcf" name="out_file1" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="filterList" value="-f "DP > 10""/>
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26 <param name="input" value="vcflib.vcf"/>
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27 <output name="out_file1" file="vcffilter-test1.vcf"/>
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28 </test>
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29 </tests>
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30 <help>
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31
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32 VCFfilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
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33
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34 You can specify the following option the **Specify filtering expression** box in any combination::
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35
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36 -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter
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37 -g, --genotype-filter specifies a filter to apply to the genotype fields of records
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38 -s, --filter-sites filter entire records, not just alleles
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39 -t, --tag-pass tag vcf records as positively filtered with this tag, print all records
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40 -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records
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41 -A, --append-filter append the existing filter tag, don't just replace it
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42 -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag
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43 -v, --invert inverts the filter, e.g. grep -v
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44 -o, --or use logical OR instead of AND to combine filters
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45
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46 Filters are specified in the form {ID} {operator} {value}::
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47
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48 -f "DP > 10" # for info fields
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49 -g "GT = 1|1" # for genotype fields
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50 -f "CpG" # for 'flag' fields
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51
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52 Operators can be any of: =, !, <, >, pipe, &
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53
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54 Any number of filters may be specified. They are combined via logical AND
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55 unless --or is specified on the command line.
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56
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57 For convenience, you can specify "QUAL" to refer to the quality of the site, even
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58 though it does not appear in the INFO fields.
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59
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60 </help>
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61 </tool>
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