Mercurial > repos > iuc > lofreq_call

annotate lofreq_call.xml @ 0:31216d510164 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
author iuc
date Tue, 17 Dec 2019 17:27:17 -0500
parents
children dfadc322b065
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31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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1 <tool id="lofreq_call" name="Call variants" version="@WRAPPER_VERSION@0">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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2 <description>with LoFreq</description>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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3 <macros>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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4 <import>macros.xml</import>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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5 </macros>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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6 <expand macro="requirements" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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7 <command detect_errors="exit_code"><![CDATA[
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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8 ## prepare reference genome and mapped reads input
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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9 @PREPARE_REF@
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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10 ln -s '$reads' reads.bam &&
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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11 ln -s -f '${reads.metadata.bam_index}' reads.bam.bai &&
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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12
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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13 ## call variants with lofreq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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14
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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15 ## make lofreq stick to tool contract by
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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16 ## generating tmp output inside job working dir
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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17 mkdir pp-tmp &&
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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18 export TMPDIR=pp-tmp &&
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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19
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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20 lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose
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21
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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22 --ref '$reference_fasta_fn' --out variants.vcf $variant_types
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23
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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24 #if str($regions.restrict_to_region) == 'regions_from_file':
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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25 --bed '$regions.bed'
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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26 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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27
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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28 #if str($call_control.set_call_options) == 'yes':
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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29 --min-cov $call_control.coverage.min_cov
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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30 --max-depth $call_control.coverage.max_depth
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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31 $call_control.pe.use_orphan
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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32 --min-bq $call_control.bc_quals.min_bq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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33 --min-alt-bq $call_control.bc_quals.min_alt_bq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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34 --def-alt-bq $call_control.bc_quals.def_alt_bq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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35 ${call_control.align_quals.alnqual.use_alnqual}
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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36 #if str($call_control.align_quals.alnqual.use_alnqual) != '-A -B':
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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37 ${call_control.align_quals.alnqual.alnqual_choice.alnquals_to_use}
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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38 ${call_control.align_quals.alnqual.alnqual_choice.extended_baq}
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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39 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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40 --min-mq $call_control.map_quals.min_mq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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41 --max-mq $call_control.map_quals.use_mq.max_mq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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42 $call_control.map_quals.use_mq.no_mq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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43 #if str($call_control.source_qual.use_src_qual.src_qual):
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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44 $call_control.source_qual.use_src_qual.src_qual
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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45 #set $ign_vcfs = ','.join([str($ign_vcf) for $ign_vcf in $call_control.source_qual.use_src_qual.ign_vcf if $ign_vcf])
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46 #if $ign_vcfs:
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47 --ign-vcf "$ign_vcfs"
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48 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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49 --def-nm-q $call_control.source_qual.use_src_qual.def_nm_q
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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50 #end if
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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51 --min-jq $call_control.joint_qual.min_jq
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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52 --min-alt-jq $call_control.joint_qual.min_alt_jq
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iuc
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53 --def-alt-jq $call_control.joint_qual.def_alt_jq
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54 #end if
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55
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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56 --sig $filter_control.sig
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57 #set $bonf_factor = $filter_control.bonf or 'dynamic'
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58 --bonf $bonf_factor
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59 $filter_control.others
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60
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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61 reads.bam 2>&1
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62
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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63 ## in case of errors add the log files produced
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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64 ## by the parallel workers to stderr
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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65 || (tool_exit_code=\$? && cat pp-tmp/lofreq2_call_parallel*/*.log 1>&2 && exit \$tool_exit_code)
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66
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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67 ## work around a bug in lofreq call-parallel
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68 ## https://github.com/CSB5/lofreq/issues/85
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69 ## that causes the output format to be vcf.gz with certain filter
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70 ## combinations.
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71 #if str($bonf_factor) != 'dynamic':
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72 #if '--no-default-filter' in str($filter_control.others):
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73 && ln -s variants.vcf variants.vcf.gz
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74 && gzip -df variants.vcf.gz
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75 #end if
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76 #end if
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77 ]]></command>
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78 <inputs>
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79 <param type="data" name="reads" format="bam" label="Input reads in BAM format" />
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80 <expand macro="reference_interface" />
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81 <conditional name="regions">
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82 <param name="restrict_to_region" type="select"
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83 label="Call variants across">
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84 <option value="genome">Whole reference</option>
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85 <option value="regions_from_file">Regions specified in BED</option>
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86 </param>
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87 <when value="genome" />
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88 <when value="regions_from_file">
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89 <param argument="--bed" type="data" format="bed"
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90 label="BED dataset with regions to examine" />
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91 </when>
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92 </conditional>
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93 <param name="variant_types" type="select"
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94 label="Types of variants to call"
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95 help="Note: When including indels in the called variants you should preprocess your input data to include indel alignment qualities">
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96 <option value="--call-indels">SNVs and indels</option>
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97 <option value="" selected="True">Only SNVs</option>
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98 <option value="--only-indels">Only indels</option>
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99 </param>
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100 <conditional name="call_control">
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101 <param name="set_call_options" type="select"
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102 label="Variant calling parameters">
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103 <option value="no">Use default settings</option>
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104 <option value="yes">Configure settings</option>
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105 </param>
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106 <when value="no" />
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107 <when value="yes">
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108 <section name="coverage" title="Coverage" expanded="true">
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109 <param name="min_cov" argument="--min-cov" type="integer" value="1" min="1"
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110 label="Minimal coverage"
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111 help="Do not attempt variant calling at sites that are not covered by at least this number of reads (default: 1)" />
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112 <param name="max_depth" argument="--max-depth" type="integer" value="1000000" min="1"
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113 label="Coverage cap"
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114 help="For efficiency, don not consider more than this number of reads at any site (default: 1,000,000)" />
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115 </section>
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116 <section name="pe" title="Paired reads" expanded="true">
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117 <param name="use_orphan" argument="--use-orphan" type="boolean" truevalue="--use-orphan" falsevalue="" checked="False"
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118 label="Use reads from anomalously mapped pairs"
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119 help="Applies to paired-end reads only. If set to true, reads from pairs that are flagged as non-proper pairs (SAM/BAM FLAG field 2) will be used in variant calling. The default is to ignore such reads." />
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120 </section>
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121 <section name="bc_quals" title="Base-calling quality" expanded="true">
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122 <param name="min_bq" argument="--min-bq" type="integer" value="6"
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123 label="Minimum baseQ"
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124 help="For variant calling at any given site, do not consider reads for which the base at that site has a base quality less than this value (default: 6)" />
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125 <param name="min_alt_bq" argument="--min-alt-bq" type="integer" min="0" value="6"
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126 label="Minimum baseQ for alternate bases"
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127 help="For variant calling at any given site, do not consider reads that support a non-reference allele at the site if that base has a base quality less than this value (default: 6). Note: this setting will have no effect if the specified value is less than the general Minimum baseQ above." />
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128 <param name="def_alt_bq" argument="--def-alt-bq" type="integer" min="0" value="0"
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129 label="Overwrite baseQs of alternate bases with this value"
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130 help="After filtering reads according to the Minimum baseQ settings above, set the base quality of the non-reference bases in the surviving reads to this new value (default: 0 = keep the original base quality)." />
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131 </section>
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132 <section name="align_quals" title="Base alignment quality" expanded="true"
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133 help="Choose here whether you want to incorporate base and/or indel alignment qualities into lofreq's joint quality model. If you have previously computed and stored (using lofreq alnqual) any of these quality scores into your input dataset, you can tell the tool to reuse them. Alternatively, the tool can calculate the necessary scores on the fly.">
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134 <conditional name="alnqual">
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135 <param name="use_alnqual" type="select"
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136 label="Consider base/indel alignment qualities during variant calling?">
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137 <option value="">Yes, and prefer existing alignment qualities encoded in input</option>
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138 <option value="--del-baq">Yes, (re)calculate alignment qualities on the fly and use them</option>
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139 <option value="-A -B">No, don't make use of alignment qualities</option>
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140 </param>
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141 <when value="">
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142 <expand macro="handle_existing_alnqual" />
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143 </when>
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144 <when value="--del-baq">
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145 <expand macro="handle_alnqual" mode="Add and use" />
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146 </when>
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147 <when value="-A -B" />
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148 </conditional>
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149 </section>
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150 <section name="map_quals" title="Mapping quality" expanded="true">
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151 <param name="min_mq" argument="--min-mq" type="integer" value="0"
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152 label="Minimum mapping quality"
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153 help="For variant calling at any given site, do not consider reads with a mapping quality (MAPQ) less than this value (default: 0 = do not filter on read mapping quality)." />
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154 <conditional name="use_mq">
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155 <param name="no_mq" argument="--no-mq" type="select"
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156 label="Consider mapping quality during variant calling?">
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157 <option value="">Yes, incorporate MAPQ into joint quality score</option>
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158 <option value="--no-mq">No, ignore MAPQ scores during variant calling</option>
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159 </param>
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160 <when value="">
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161 <param name="max_mq" argument="--max-mq" type="integer" value="255"
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162 label="Maximum mapping quality"
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163 help="For the joint quality model at any site, cap the mapping quality of reads at this value (default: 255 = do not cap mapping qualities). Note: The special MAPQ value 255 is used by many tools to indicate undefined mapping quality, and lofreq call will ignore such reads during variant calling. Capping, however, will turn 255 into a regular MAPQ score. Thus, if you need to avoid using such reads, you should filter out MAPQ 255 reads from your input data with other tools before using lofreq call with MAPQ capping."/>
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164 </when>
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165 <when value="--no-mq">
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166 <param name="max_mq" type="hidden" value="" />
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167 </when>
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168 </conditional>
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169 </section>
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170 <section name="source_qual" title="Source quality" expanded="true">
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171 <conditional name="use_src_qual">
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172 <param argument="--src-qual" name="src_qual" type="select"
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173 label="Compute source quality and consider it during variant calling">
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174 <option value="">No, don't incorporate source quality into joint quality score</option>
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175 <option value="--src-qual">Yes, compute source quality and merge it into joint quality score</option>
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176 </param>
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177 <when value="" />
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178 <when value="--src-qual">
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179 <param name="def_nm_q" argument="--def-nm-q" type="integer" min="-1" value="-1"
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180 label="Replace non-match base qualities with this value"
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181 help="For the calculation of the source quality, replace all base qualities of non-match bases with this value (default: -1 = use original base qualities)." />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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182 <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf" optional="true" multiple="true"
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183 label="VCF input(s) with variants to ignore for source quality computation"
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184 help="Mismatches caused by known true variants in your samples should not lower the source quality estimate. If any read in your input has a base that is non-reference, but supports one of the known variants in the specified VCF datasets, that base will not be treated as a mismatch." />
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185 </when>
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186 </conditional>
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187 </section>
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188 <section name="joint_qual" title="Joint quality" expanded="true">
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189 <param name="min_jq" argument="--min-jq" type="integer" min="0" value="0"
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190 label="Minimum joinedQ"
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191 help="At any site, do not use reads for variant calling, if their calculated joint quality at that site is lower than this value (default: 0 = do not filter based on joint quality)" />
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192 <param name="min_alt_jq" argument="--min-alt-jq" type="integer" min="0" value="0"
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193 label="Minimum joinedQ for alternate bases"
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194 help="At any site, do not use reads for variant calling, if they support a non-reference allele at that site and their calculated joint quality at the site is lower than this value (default: 0 = do not filter based on joint quality). Note: this setting has no effect if the specified value is smaller than the general Minimum joinedQ set above." />
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195 <!-- def-alt-jq==-1, though documented, is currently not implemented -->
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196 <param name="def_alt_jq" argument="--def-alt-jq" type="integer" min="0" value="0"
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197 label="Overwrite joinedQs of alternate bases with this value"
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198 help="After filtering according to the Minimum joinedQ settings above, set the joint quality values for all reads surviving filtering and supporting a non-reference allele to this value (default: 0 = use the original calculated joint quality)." />
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diff changeset
199 </section>
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200 </when>
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201 </conditional>
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202 <conditional name="filter_control">
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203 <param name="filter_type" type="select"
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diff changeset
204 label="Variant filter parameters">
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205 <option value="set_all_off">Strictly no filtering</option>
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206 <option value="set_no_default">Preset QUAL score-based filtering</option>
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207 <option value="set_lofreq_standard" selected="true">Preset filtering on QUAL score + coverage + strand bias (lofreq call default)</option>
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208 <option value="set_custom">Custom filter settings/combinations</option>
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209 </param>
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210 <when value="set_all_off">
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211 <param name="sig" type="hidden" value="1" />
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212 <param name="bonf" type="hidden" value="1" />
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213 <param name="others" type="hidden" value="--no-default-filter" />
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214 </when>
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215 <when value="set_no_default">
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216 <param name="sig" type="hidden" value="0.01" />
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217 <param name="bonf" type="hidden" value="dynamic" />
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218 <param name="others" type="hidden" value="--no-default-filter" />
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219 </when>
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220 <when value="set_lofreq_standard">
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221 <param name="sig" type="hidden" value="0.01" />
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222 <param name="bonf" type="hidden" value="dynamic" />
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223 <param name="others" type="hidden" value="" />
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224 </when>
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225 <when value="set_custom">
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226 <param name="sig" type="float" value="0.01" min="0" max="1"
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227 label="Significance threshold for calls"/>
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228 <param name="bonf" type="integer" value="0" min="0"
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229 label="Bonferroni correction factor for multiple testing"
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230 help="Set to zero to determine dynamically from actual number of variant tests performed. Dynamic detection will calculate separate correction factors for SNVs and indels" />
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231 <param name="others" type="boolean" truevalue="" falsevalue="--no-default-filter" checked="true"
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232 label="Apply default coverage and strand-bias filter?"
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233 help="" />
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234 </when>
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235 </conditional>
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236 </inputs>
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237 <outputs>
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238 <data name="variants" from_work_dir="variants.vcf" format="vcf" />
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239 </outputs>
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240 <tests>
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241 <test>
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242 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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243 <param name="ref_selector" value="history" />
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244 <param name="ref" ftype="fasta" value="pBR322.fa" />
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245 <output name="variants" file="call-out1.vcf" lines_diff="4" />
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246 </test>
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247 <test>
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248 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
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249 <param name="ref_selector" value="history" />
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iuc
parents:
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250 <param name="ref" ftype="fasta" value="pBR322.fa" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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251 <conditional name="filter_control">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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252 <param name="filter_type" value="set_all_off" />
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253 </conditional>
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parents:
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254 <output name="variants" file="call-out2.vcf" lines_diff="4" />
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255 </test>
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256 </tests>
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parents:
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257 <help><![CDATA[
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258 lofreq call: call variants from BAM file
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259
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
260 LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
261 from next-generation sequencing data. It makes full use of base-call qualities
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
262 and other sources of errors inherent in sequencing, which are usually ignored
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
263 by other methods or only used for filtering.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
264
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
265 LoFreq can run on almost any type of aligned sequencing data since no machine-
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
266 or sequencing-technology dependent thresholds are used. It automatically adapts
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
267 to changes in coverage and sequencing quality and can therefore be applied to a
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
268 variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
269 somatic data.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
270
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
271 While the tool will often give reasonable results with default settings a
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
272 variety of options let you control its exact behavior. These advanced options
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
273 can be subdivided into those affecting variant calling and those affecting
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
274 posterior filtering of the results.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
275
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
276 **Variant calling paramters**
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
277
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
278 At the heart of LoFreq's variant caller is a **joint quality score** that is
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
279 computed for every site in every read (that survives filtering) and that
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
280 combines some or all of the following read and base quality measures:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
281
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
282 - Base/indel quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
283
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
284 For any read, this is the Phred-scaled likelihood that the base mapped to a
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
285 given site does not represent a sequencing error. For every base, this score
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
286 got computed by the base caller of your sequencing platform and got
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
287 incorporated into your input dataset during read alignment.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
288
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
289 For insertions/deletions this is defined, analogously, as the Phred-scaled
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
290 likelihood that any inserted/deleted base is real, however, you are
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
291 responsible for adding indel qualitites, which are required for indel
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
292 calling with lofreq, to your input.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
293
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
294 For doing so, you can use ``lofreq indelqual`` or GATK's BQSR.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
295
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
296 - Base/indel alignment quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
297
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
298 For any read, this is the Phred-scaled likelihood that the read's base or
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
299 indel mapped to a given reference genome position is mapped to this position
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
300 correctly.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
301
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
302 The tool can calculate these scores for you on the fly. Alternatively, you
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
303 can precalculate them using ``lofreq alnqual``, which will incorporate them
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
304 into your input dataset.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
305
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
306 - Mapping quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
307
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
308 The Phred-scaled likelihood that the read got mapped to the correct place
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
309 in the reference genome. This score got incorporated into your input dataset
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
310 by the aligner you used to map your reads.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
311
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
312 - Source quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
313
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
314 This is the Phred-scaled likelihood that the given read comes from the
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
315 reference genome. The tool can calculate this score for you.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
316
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
317
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
318 **Variant filter parameters**
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
319
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
320 After generating a list of called variants, the tool can filter this list
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
321 based on:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
322
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
323 - the statistical significance of the variant calls
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
324 - strand-bias of reads supporting the variant
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
325 - coverage of the variant site
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
326
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
327 While posterior filtering can help reduce false-positive variant calls, please
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
328 note that the separate ``lofreq filter``, which can be run on the output of
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
329 ``lofreq call`` has many more options for configuring filters.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
330
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
331 These are the different filter settings supported by the tool:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
332
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
333 *Preset filtering on QUAL score + coverage + strand bias*
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
334
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
335 For variants to pass this filter, the following is required:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
336
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
337 - statistical signficance of the variant call with a pvalue < 0.01 based on the
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
338 retransformed QUAL score of the variant and multiple-testing corrected using
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
339 a dynamically determined Bonferroni factor (based on the number of overall
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
340 variants considered during calling).
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
341
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
342 - A strand-bias in supporting reads not significant under a FDR-corrected p
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
343 value of 0.001 and 85% of supporting reads mapped to the same strand of the
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
344 genome.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
345
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
346 - A coverage of the variant site of at least 10x.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
347
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
348 *Preset QUAL score-based filtering*
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
349
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
350 Same QUAL-based significance filter as the default, but without the strand-bias
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
351 and coverage criteria
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
352
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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353 *Strictly no filtering*
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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354
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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355 Do not apply any filters, but produce the original list of all called variants.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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356 You will almost always want to use ``lofreq filter`` to process the resulting
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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357 output.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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358
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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359 *Custom filter settings/combinations*
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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360
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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361 Lets you define your own QUAL-based significance filter and, optionally,
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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362 combine it with the default starnd-bias and coverage filters.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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363 ]]></help>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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364 <expand macro="citations" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
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365 </tool>