Mercurial > repos > wolma > mimodd_main
annotate deletion_predictor.xml @ 1:bfcd121b99bf draft default tip
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 44e872b808f88eacd05963fc2478da2c07b50228
author | wolma |
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date | Thu, 22 Mar 2018 10:32:39 -0400 |
parents | f0f2795de2c7 |
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rev | line source |
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f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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1 <tool id="mimodd_delcall" name="MiModD Deletion Calling (for PE data)" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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2 version="@MIMODD_WRAPPER_VERSION@"> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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3 <description> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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4 predicts deletions in one or more aligned paired-end read samples based on coverage of the reference genome and on insert sizes |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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5 </description> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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6 <macros> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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7 <import>macros.xml</import> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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8 </macros> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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9 <expand macro="requirements" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
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10 <expand macro="stdio" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
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11 <expand macro="version_command" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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12 <command><![CDATA[ |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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13 mimodd delcall |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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14 #for $bam_file in $list_input |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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15 '$bam_file' |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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16 #end for |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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17 '$covfile' -o '$ofile' |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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18 --index-files |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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19 #for $bam_file in $list_input |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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20 '${bam_file.metadata.bam_index}' |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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21 #end for |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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22 --max-cov $max_cov --min-size $min_size |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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23 $include_uncovered |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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24 $group_by_id |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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25 --verbose |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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26 ]]></command> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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27 |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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28 <inputs> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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29 <param name="list_input" type="data" multiple="true" format="bam" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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30 label="Aligned reads input dataset(s)" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
parents:
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31 <param name="covfile" type="data" format="bcf" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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32 label="BCF variant call dataset to extract coverage from" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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33 help="Use the MiModD Variant Calling Tool to generate this file."/> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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34 <param name="group_by_id" type="boolean" truevalue="-i" falsevalue="" checked="false" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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35 label="group reads based on read group id only" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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36 help="If selected, reads from different read groups will be treated strictly separate. If turned off, read groups with identical sample names are used together for identifying uncovered regions, but are still treated separately for the prediction of deletions." /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
wolma
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37 <param name="include_uncovered" type="boolean" truevalue="-u" falsevalue="" checked="false" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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38 label="include low-coverage regions" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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39 help="If selected, regions that fulfill the coverage criteria below, but are not statistically significant deletions, will be included in the output." /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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40 <param name="max_cov" type="integer" value="0" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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41 label="maximal coverage allowed inside a low-coverage region (default: 0)" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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42 help="The maximal coverage at a site allowed to consider it as part of a low-coverage region" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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43 <param name="min_size" type="integer" value="100" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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44 label="minimal deletion size (default: 100)" |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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45 help="A low-coverage region must consist of at least this number of consecutive bases below the maximal coverage to consider it in further analyses."/> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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46 </inputs> |
f0f2795de2c7
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47 |
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48 <outputs> |
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49 <data name="ofile" format="gff" /> |
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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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50 </outputs> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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51 |
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52 <tests> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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53 <test> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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54 <param name="list_input" value="a.bam" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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55 <param name="covfile" value="a.bcf" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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56 <param name="include_uncovered" value="true" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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57 <assert_command> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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58 <has_text text=" -u " /> |
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59 <not_has_text text=" -i " /> |
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60 </assert_command> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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61 <output name="ofile" ftype="gff"> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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62 <assert_contents> |
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63 <has_n_columns n="9" /> |
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64 <has_line_matching |
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65 expression="^chrI	MiModD	Uncovered_Region.+" /> |
f0f2795de2c7
planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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66 <has_line_matching |
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67 expression="^chrII	MiModD	Uncovered_Region.+" /> |
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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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68 <has_line_matching |
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69 expression="^chrIII	MiModD	Uncovered_Region.+" /> |
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70 <has_line_matching |
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71 expression="^chrIV	MiModD	Uncovered_Region.+" /> |
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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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72 <has_line_matching |
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73 expression="^chrV	MiModD	Uncovered_Region.+" /> |
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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
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74 <has_line_matching |
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75 expression="^chrX	MiModD	Uncovered_Region.+" /> |
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76 <has_line_matching |
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77 expression="^MtDNA	MiModD	Uncovered_Region.+" /> |
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78 </assert_contents> |
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79 </output> |
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80 </test> |
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81 </tests> |
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82 |
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83 <help><![CDATA[ |
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84 .. class:: infomark |
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85 |
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86 **What it does** |
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87 |
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88 The tool predicts deletions from paired-end data in a two-step process: |
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89 |
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90 1) It finds regions of low-coverage, i.e., candidate regions for deletions, by scanning a BCF file produced by the *Variant Calling* tool. |
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91 |
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92 The *maximal coverage allowed inside a low-coverage region* and the *minimal deletion size* parameters are used at this step to define what is considered a low-coverage region. |
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93 |
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94 .. class:: warningmark |
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95 |
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96 The tool treats genome positions missing from the BCF input as zero coverage, so it is safe to use ONLY with BCF files produced by the *Variant Calling* tool or through other commands that keep the information for all sites. |
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97 |
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98 2) It assesses every low-coverage region statistically for evidence of it being a real deletion. **This step requires paired-end data** since it relies on shifts in the distribution of read pair insert sizes around real deletions. |
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99 |
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100 By default, the tool only reports Deletions, i.e., the subset of low-coverage regions that pass the statistical test. |
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101 If *include low-coverage regions* is selected, regions that failed the test will also be reported. |
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102 |
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103 With *group reads based on read group id only* selected, as it is by default, grouping of reads into samples is done strictly based on their read group IDs. |
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104 With the option deselected, grouping is done based on sample names in the first step of the analysis, i.e. the reads of all samples with a shared sample name are used to identify low-coverage regions. |
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105 In the second step, however, reads will be regrouped by their read group IDs again, i.e. the statistical assessment for real deletions is always done on a per read group basis. |
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106 |
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107 **TIP:** |
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108 Deselecting *group reads based on read group id only* can be useful, for example, if you have both paired-end and single-end sequencing data for the same sample. |
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109 |
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110 In this case, the two sets of reads will usually share a common sample name, but differ in their read groups. |
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111 With grouping based on sample names, the single-end data can be used together with the paired-end data to identify low-coverage regions, thus increasing overall coverage and reliability of this step. |
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112 Still, the assessment of deletions will use only the paired-end data (auto-detecting that the single-end reads do not provide insert size information). |
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113 |
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114 @HELP_FOOTER@ |
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115 ]]></help> |
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116 <expand macro="citations" /> |
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117 </tool> |