Mercurial > repos > iuc > tb_variant_filter
annotate tb_variant_filter.xml @ 4:e7aff4a85df5 draft
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 94fac53d84d560d45ccc94c9143674edbf9213c8"
author | iuc |
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date | Sun, 29 Aug 2021 21:46:17 +0000 |
parents | 40f0591deda0 |
children | ee4a90760848 |
rev | line source |
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4
e7aff4a85df5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 94fac53d84d560d45ccc94c9143674edbf9213c8"
iuc
parents:
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1 <tool id="tb_variant_filter" name="TB Variant Filter" version="@TOOL_VERSION@+galaxy2" profile="20.09"> |
0
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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2 <description>M. tuberculosis H37Rv VCF filter</description> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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3 <macros> |
2
e5c84ba20d99
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ffff6c2b9a2a83256779a719397b333d2f7ae42e"
iuc
parents:
1
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4 <token name="@TOOL_VERSION@">0.3.5</token> |
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3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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5 </macros> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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6 <requirements> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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7 <requirement type="package" version="@TOOL_VERSION@">tb_variant_filter</requirement> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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8 </requirements> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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9 <command detect_errors="exit_code"><![CDATA[ |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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10 tb_variant_filter |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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11 #if "region_filter" in str($filters).split(',') |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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12 #if str($filter_options.show_filter_options) == "yes": |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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13 --region_filter $filter_options.region_filter |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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14 #else |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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15 --region_filter pe_ppe,uvp |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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16 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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17 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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18 #if "close_to_indel_filter" in str($filters).split(',') |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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19 --close_to_indel_filter |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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20 #if str($filter_options.show_filter_options) == "yes": |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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21 --indel_window_size $filter_options.indel_window_size |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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22 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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23 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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24 #if "min_percentage_alt_filter" in str($filters).split(',') |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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25 --min_percentage_alt_filter |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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26 #if str($filter_options.show_filter_options) == "yes": |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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27 --min_percentage_alt $filter_options.min_percentage_alt |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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28 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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29 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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30 #if "min_depth_filter" in str($filters).split(',') |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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31 --min_depth_filter |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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32 #if str($filter_options.show_filter_options) == "yes": |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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33 --min_depth $filter_options.min_depth |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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34 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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35 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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36 #if "snv_only_filter" in str($filters).split(','): |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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37 --snv_only_filter |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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38 #end if |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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39 '$input1' '$output1' |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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40 ]]></command> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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41 <inputs> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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42 <param type="data" name="input1" label="VCF file to be filter" format="vcf"/> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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43 |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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44 <param type="select" name="filters" multiple="true" label="Filters to apply"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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45 <option value="region_filter" selected="true">Filter out variants by regions</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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46 <option value="close_to_indel_filter">Filter variants close to indels</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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47 <option value="min_percentage_alt_filter">Filter variants by percentage alt allele</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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48 <option value="min_depth_filter">Filter sites by read alignment depth</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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49 <option value="snv_only_filter">Only accept SNVs</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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50 </param> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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51 |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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52 <conditional name="filter_options"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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53 <param type="select" name="show_filter_options" label="Show options for the filters"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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54 <option value="yes">Yes</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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55 <option value="no" selected="true">No</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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56 </param> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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57 <when value="yes"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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58 <param argument="--region_filter" type="select" multiple="true" label="Region filters to enable"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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59 <!-- if these are changed the code above needs to change to keep the defaults in line with those that are default here --> |
1
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
iuc
parents:
0
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60 <option value="farhat_rlc">Refined Low Confidence regions from Farhat lab</option> |
0
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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61 <option value="pe_ppe" selected="true">PE/PPE</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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62 <option value="tbprofiler">TBProfiler antibiotic resistant genes</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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63 <option value="mtbseq">MTBseq antibiotic resistant genes</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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64 <option value="uvp" selected="true">UVP repeat / insertion sequence sites</option> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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65 </param> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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66 <param argument="--indel_window_size" type="integer" value="5" label="Window to mask around indels"/> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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67 <param argument="--min_percentage_alt" type="float" value="90" |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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68 label="Minimum alternate allele percentage to accept"/> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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69 <param argument="--min_depth" type="integer" value="30" label="Minimum read depth (coverage)"/> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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70 </when> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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71 <when value="no"></when> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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72 |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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73 </conditional> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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74 </inputs> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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75 <outputs> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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76 <data name="output1" format="vcf"/> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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77 </outputs> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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78 <tests> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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79 <test> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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80 <param name="input1" value="test_input1.vcf" ftype="vcf" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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81 <param name="filters" value="region_filter" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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82 <conditional name="filter_options"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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83 <param name="show_filter_options" value="yes" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
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84 <param name="region_filter" value="pe_ppe,tbprofiler,uvp" /> |
3b1e7c170b10
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85 </conditional> |
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86 <output name="output1" file="test_output1.vcf" ftype="vcf" /> |
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87 </test> |
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88 <test> |
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89 <param name="input1" value="test_input1.vcf" ftype="vcf" /> |
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90 <param name="filters" value="close_to_indel_filter" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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91 <conditional name="filter_options"> |
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92 <param name="show_filter_options" value="yes" /> |
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93 <param name="indel_window_size" value="5" /> |
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94 </conditional> |
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95 <output name="output1" file="test_output2.vcf" ftype="vcf" /> |
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96 </test> |
3b1e7c170b10
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97 <test> |
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98 <param name="input1" value="test_input1.vcf" ftype="vcf" /> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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99 <param name="filters" value="min_percentage_alt_filter" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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100 <conditional name="filter_options"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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101 <param name="show_filter_options" value="yes" /> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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102 <param name="min_percentage_alt" value="95.0" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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103 </conditional> |
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104 <output name="output1" file="test_output3.vcf" ftype="vcf" /> |
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105 </test> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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106 <test> |
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107 <param name="input1" value="test_input2.vcf" ftype="vcf" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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108 <param name="filters" value="min_percentage_alt_filter" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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109 <conditional name="filter_options"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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110 <param name="show_filter_options" value="yes" /> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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111 <param name="min_percentage_alt" value="30.0" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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112 </conditional> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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113 <output name="output1" file="test_output4.vcf" ftype="vcf" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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114 </test> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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115 <test> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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116 <param name="input1" value="test_input1.vcf" ftype="vcf" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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117 <param name="filters" value="min_depth_filter" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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118 <conditional name="filter_options"> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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119 <param name="show_filter_options" value="yes" /> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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120 <param name="min_depth" value="30" /> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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121 </conditional> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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122 <output name="output1" file="test_output5.vcf" ftype="vcf" /> |
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123 </test> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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124 <test> |
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125 <param name="input1" value="test_input1.vcf" ftype="vcf" /> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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126 <param name="filters" value="snv_only_filter" /> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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127 <output name="output1" file="test_output6.vcf" ftype="vcf" /> |
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128 </test> |
1
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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129 <test> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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130 <param name="input1" value="test_input1.vcf" ftype="vcf" /> |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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|
131 <param name="filters" value="region_filter" /> |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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|
132 <conditional name="filter_options"> |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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133 <param name="show_filter_options" value="yes" /> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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134 <param name="region_filter" value="farhat_rlc" /> |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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135 </conditional> |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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|
136 <assert_stderr> |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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|
137 <has_text text="masked: 2" /> |
3
40f0591deda0
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ccc6fdea9d13ad731c193577c4c901de1ff1fda8"
iuc
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2
diff
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|
138 </assert_stderr> |
1
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
iuc
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|
139 </test> |
0
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
140 </tests> |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
141 <help><![CDATA[ |
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142 This tool offers multiple options for filtering variants (in |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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parents:
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|
143 VCF files, relative to M. tuberculosis H37Rv). |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
144 |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
145 It currently has 5 main modes: |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
146 |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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147 1. Filter by region. Mask out variants in certain regions. Region lists available as: |
1
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
iuc
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|
148 1. Refined Low Confidence (RLC) regions from `Marin et al 2021 <https://www.biorxiv.org/content/10.1101/2021.04.08.438862v1.full>`_ |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
iuc
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|
149 2. PE/PPE genes from `Fishbein et al 2015 <https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.12981>`_ |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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|
150 3. `TBProfiler <http://tbdr.lshtm.ac.uk/>`_ list of antibiotic resistant genes |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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|
151 4. `MTBseq <https://github.com/ngs-fzb/MTBseq_source>`_ list of antibiotic resistant genes |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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|
152 5. `UVP <https://github.com/CPTR-ReSeqTB/UVP>`_ list of repetitive loci in M. tuberculosis genome |
0
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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153 2. Filter by window around indels. Masks out variants within a certain distance (by default 5 bases) of an insertion or deletion site. |
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154 3. Filter by percentage of alternate allele bases. Mask out variants with less than a minimum percentage (by default 90%) alternative alleles. |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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155 4. Filter by depth of aligned reads. |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
156 5. Filter out all variants that are not SNV (single nucleotide variants). |
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"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
157 |
1
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
iuc
parents:
0
diff
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|
158 For region filtering, the default choice is to use the PE/PPE and UVP regions to mask out variants. `Marin et al 2021 <https://www.biorxiv.org/content/10.1101/2021.04.08.438862v1.full>`_ |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
iuc
parents:
0
diff
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|
159 from Prof Maha Farhat's lab make a persuasive argument that their smaller list of Refined Low Confidence (RLC) regions is a better argument but this work has not yet been peer |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
iuc
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0
diff
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|
160 review so it is included as an option that is not currently the default. |
eee2da03d1f5
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit ef1b4164979078a6624c5b81fa156755258fb5f8"
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0
diff
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|
161 |
0
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
162 When used together the effects of the filters are added (i.e. a variant is masked out if it is masked by any of the filters). |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
163 ]]></help> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
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diff
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|
164 <citations> |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
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|
165 <citation type="bibtex"><![CDATA[ |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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|
166 @misc{vanHeusden2019, |
3b1e7c170b10
"planemo upload for repository https://github.com/COMBAT-TB/tb_variant_filter commit 36771827ae3d5dc06df488b3faffb392f77e672e"
iuc
parents:
diff
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|
167 author = {van Heusden, P.}, |
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168 title = {tb_variant_filter}, |
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169 year = {2019}, |
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170 publisher = {GitHub}, |
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171 journal = {GitHub repository}, |
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172 howpublished = {\url{https://github.com/pvanheus/tb_variant_filter}}, |
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173 commit = {4a9b2a4a85ddbfbb0d713a02373c8aa0aa159a6c} |
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174 } |
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175 ]]></citation> |
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176 </citations> |
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177 </tool> |