Mercurial > repos > iuc > lofreq_call

annotate lofreq_call.xml @ 7:4805fe3d8fda draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
author iuc
date Wed, 06 Jul 2022 09:25:57 +0000
parents e1461b5c52a0
children b11e8e9c23bf
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7
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
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1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy2" profile="18.01">
0
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2 <description>with LoFreq</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 ## prepare reference genome and mapped reads input
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9 @PREPARE_REF@
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10 ln -s '$reads' reads.bam &&
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11 ln -s -f '${reads.metadata.bam_index}' reads.bam.bai &&
2
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12 #if str($call_control.set_call_options) == 'yes':
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13 #set $ign_vcfs = []
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14 #if str($call_control.source_qual.use_src_qual.src_qual):
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15 #for $n, $ign_vcf in enumerate($call_control.source_qual.use_src_qual.ign_vcf):
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16 ## lofreq recognizes compressed vcf input based on its .gz
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17 ## suffix => symlink all datasets with standard extensions.
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18 ## For bgzipped vcfs, also make the index files available.
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19 #if $ign_vcf:
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20 #if $ign_vcf.is_of_type('vcf_bgzip'):
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21 #set $ign_src = 'ign%d.vcf.gz' % $n
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22 ln -s '$ign_vcf' $ign_src &&
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23 ln -s '$ign_vcf.metadata.tabix_index' ${ign_src}.tbi &&
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24 #else:
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25 #set $ign_src = 'ign%d.vcf' % $n
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26 ln -s '$ign_vcf' $ign_src &&
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27 #end if
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28 #silent $ign_vcfs.append($ign_src)
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29 #end if
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30 #end for
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31 #end if
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32 #set $ign_vcfs = ','.join($ign_vcfs)
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33 #end if
0
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34
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35 ## call variants with lofreq
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36
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37 lofreq call-parallel --pp-threads \${GALAXY_SLOTS:-1} --verbose
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38
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39 --ref '$reference_fasta_fn' --out variants.vcf $variant_types
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40
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41 #if str($regions.restrict_to_region) == 'regions_from_file':
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42 --bed '$regions.bed'
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43 #end if
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44
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45 #if str($call_control.set_call_options) == 'yes':
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46 --min-cov $call_control.coverage.min_cov
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47 --max-depth $call_control.coverage.max_depth
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48 $call_control.pe.use_orphan
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49 --min-bq $call_control.bc_quals.min_bq
2
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50 #if $call_control.bc_quals.min_alt_bq > $call_control.bc_quals.min_bq:
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51 --min-alt-bq $call_control.bc_quals.min_alt_bq
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52 #else:
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53 --min-alt-bq $call_control.bc_quals.min_bq
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54 #end if
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55 #if str($call_control.bc_quals.alt_bq.modify):
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56 --def-alt-bq $call_control.bc_quals.alt_bq.def_alt_bq
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57 #end if
0
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58 ${call_control.align_quals.alnqual.use_alnqual}
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59 #if str($call_control.align_quals.alnqual.use_alnqual) != '-A -B':
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60 ${call_control.align_quals.alnqual.alnqual_choice.alnquals_to_use}
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61 ${call_control.align_quals.alnqual.alnqual_choice.extended_baq}
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62 #end if
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63 --min-mq $call_control.map_quals.min_mq
2
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64 #if str($call_control.map_quals.use_mq.no_mq):
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65 $call_control.map_quals.use_mq.no_mq
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66 #else:
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67 #if $call_control.map_quals.use_mq.max_mq > $call_control.map_quals.min_mq:
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68 --max-mq $call_control.map_quals.use_mq.max_mq
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69 #else:
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70 --max-mq $call_control.map_quals.min_mq
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71 #end if
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72 #end if
0
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73 #if str($call_control.source_qual.use_src_qual.src_qual):
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74 $call_control.source_qual.use_src_qual.src_qual
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75 #if $ign_vcfs:
2
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76 --ign-vcf '$ign_vcfs'
0
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77 #end if
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78 --def-nm-q $call_control.source_qual.use_src_qual.def_nm_q
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79 #end if
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80 --min-jq $call_control.joint_qual.min_jq
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81 --min-alt-jq $call_control.joint_qual.min_alt_jq
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82 --def-alt-jq $call_control.joint_qual.def_alt_jq
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83 #end if
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84
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85 --sig $filter_control.sig
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86 #set $bonf_factor = $filter_control.bonf or 'dynamic'
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87 --bonf $bonf_factor
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88 $filter_control.others
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89
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90 reads.bam 2>&1
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91
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92 ## in case of errors add the log files produced
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93 ## by the parallel workers to stderr
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94 || (tool_exit_code=\$? && cat "\$TMPDIR/lofreq2_call_parallel*/*.log" 1>&2 && exit \$tool_exit_code)
0
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95
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96 ## work around a bug in lofreq call-parallel
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97 ## https://github.com/CSB5/lofreq/issues/85
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98 ## that causes the output format to be vcf.gz with certain filter
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99 ## combinations. Issue is closed but still not fixed.
0
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100 #if str($bonf_factor) != 'dynamic':
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101 #if '--no-default-filter' in str($filter_control.others):
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102 && ln -s variants.vcf variants.vcf.gz
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103 && gzip -df variants.vcf.gz
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104 #end if
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105 #end if
7
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106 && echo $filter_control.filter_type
0
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107 ]]></command>
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108 <inputs>
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109 <param type="data" name="reads" format="bam" label="Input reads in BAM format" />
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110 <expand macro="reference_interface" />
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111 <conditional name="regions">
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112 <param name="restrict_to_region" type="select"
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113 label="Call variants across">
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114 <option value="genome">Whole reference</option>
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115 <option value="regions_from_file">Regions specified in BED</option>
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116 </param>
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117 <when value="genome" />
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118 <when value="regions_from_file">
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119 <param argument="--bed" type="data" format="bed"
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120 label="BED dataset with regions to examine" />
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121 </when>
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122 </conditional>
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123 <param name="variant_types" type="select"
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124 label="Types of variants to call"
3
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125 help="Note: To have indels included in the called variants you HAVE to preprocess your input data using lofreq indelqual to include indel qualities. In addition, it is highly recommended that you calculate and make use of indel alignment qualities. See the detailed tool help below.">
0
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126 <option value="--call-indels">SNVs and indels</option>
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127 <option value="" selected="True">Only SNVs</option>
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128 <option value="--call-indels --only-indels">Only indels</option>
0
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129 </param>
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130 <conditional name="call_control">
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131 <param name="set_call_options" type="select"
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132 label="Variant calling parameters">
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133 <option value="no">Use default settings</option>
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134 <option value="yes">Configure settings</option>
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135 </param>
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136 <when value="no" />
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137 <when value="yes">
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138 <section name="coverage" title="Coverage" expanded="true">
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139 <param name="min_cov" argument="--min-cov" type="integer" value="1" min="1"
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140 label="Minimal coverage"
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141 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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142 <param name="max_depth" argument="--max-depth" type="integer" value="1000000" min="1"
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143 label="Coverage cap"
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144 help="For efficiency, don not consider more than this number of reads at any site (default: 1,000,000)" />
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145 </section>
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146 <section name="pe" title="Paired reads" expanded="true">
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147 <param name="use_orphan" argument="--use-orphan" type="boolean" truevalue="--use-orphan" falsevalue="" checked="False"
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148 label="Use reads from anomalously mapped pairs"
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149 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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150 </section>
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151 <section name="bc_quals" title="Base-calling quality" expanded="true">
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152 <param name="min_bq" argument="--min-bq" type="integer" value="6"
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153 label="Minimum baseQ"
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154 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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155 <param name="min_alt_bq" argument="--min-alt-bq" type="integer" min="0" value="6"
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156 label="Minimum baseQ for alternate bases"
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157 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." />
2
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158 <conditional name="alt_bq">
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159 <param name="modify" type="select"
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160 label="Base quality to use for alternate bases"
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161 help="After filtering reads according to the Minimum baseQ settings above, you can choose to modify the base qualities of the non-reference bases in the surviving reads before performing further calculations.">
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162 <option value="">Use original base qualities</option>
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163 <option value="avg">Use the median of the reference base qualities at the site</option>
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164 <option value="custom">Use a fixed custom value</option>
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165 </param>
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166 <when value="" />
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167 <when value="avg">
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168 <param name="def_alt_bq" type="hidden" value="-1" />
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169 </when>
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170 <when value="custom">
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171 <param name="def_alt_bq" argument="--def-alt-bq" type="integer" min="1" value="1"
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diff changeset
172 label="Overwrite original base qualities with this value" />
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173 </when>
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174 </conditional>
0
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175 </section>
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176 <section name="align_quals" title="Base alignment quality" expanded="true"
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177 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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178 <conditional name="alnqual">
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179 <param name="use_alnqual" type="select"
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180 label="Consider base/indel alignment qualities during variant calling?">
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181 <option value="">Yes, and prefer existing alignment qualities encoded in input</option>
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182 <option value="--del-baq">Yes, (re)calculate alignment qualities on the fly and use them</option>
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183 <option value="-A -B">No, don't make use of alignment qualities</option>
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184 </param>
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185 <when value="">
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186 <expand macro="handle_existing_alnqual" />
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187 </when>
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188 <when value="--del-baq">
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189 <expand macro="handle_alnqual" mode="Add and use" />
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190 </when>
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191 <when value="-A -B" />
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192 </conditional>
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193 </section>
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194 <section name="map_quals" title="Mapping quality" expanded="true">
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195 <param name="min_mq" argument="--min-mq" type="integer" value="0"
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196 label="Minimum mapping quality"
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197 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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198 <conditional name="use_mq">
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199 <param name="no_mq" argument="--no-mq" type="select"
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200 label="Consider mapping quality during variant calling?">
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201 <option value="">Yes, incorporate MAPQ into joint quality score</option>
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202 <option value="--no-mq">No, ignore MAPQ scores during variant calling</option>
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203 </param>
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204 <when value="">
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205 <param name="max_mq" argument="--max-mq" type="integer" value="255"
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206 label="Maximum mapping quality"
2
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207 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). Notes: 1) You cannot cap mapping qualities at less than the minimum MAPQ defined above. If you try, MAPQs will be capped at that minimum quality instead. 2) 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."/>
0
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208 </when>
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209 <when value="--no-mq">
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210 <param name="max_mq" type="hidden" value="" />
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211 </when>
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212 </conditional>
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213 </section>
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214 <section name="source_qual" title="Source quality" expanded="true">
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215 <conditional name="use_src_qual">
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216 <param argument="--src-qual" name="src_qual" type="select"
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217 label="Compute source quality and consider it during variant calling">
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218 <option value="">No, don't incorporate source quality into joint quality score</option>
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219 <option value="--src-qual">Yes, compute source quality and merge it into joint quality score</option>
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220 </param>
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221 <when value="" />
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222 <when value="--src-qual">
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223 <param name="def_nm_q" argument="--def-nm-q" type="integer" min="-1" value="-1"
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224 label="Replace non-match base qualities with this value"
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225 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)." />
2
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226 <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf,vcf_bgzip" optional="true" multiple="true"
0
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227 label="VCF input(s) with variants to ignore for source quality computation"
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228 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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229 </when>
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230 </conditional>
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231 </section>
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232 <section name="joint_qual" title="Joint quality" expanded="true">
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233 <param name="min_jq" argument="--min-jq" type="integer" min="0" value="0"
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234 label="Minimum joinedQ"
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235 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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236 <param name="min_alt_jq" argument="--min-alt-jq" type="integer" min="0" value="0"
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237 label="Minimum joinedQ for alternate bases"
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238 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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239 <!-- def-alt-jq==-1, though documented, is currently not implemented -->
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240 <param name="def_alt_jq" argument="--def-alt-jq" type="integer" min="0" value="0"
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241 label="Overwrite joinedQs of alternate bases with this value"
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242 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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243 </section>
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244 </when>
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245 </conditional>
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246 <conditional name="filter_control">
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247 <param name="filter_type" type="select"
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248 label="Variant filter parameters">
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249 <option value="set_all_off">Strictly no filtering</option>
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250 <option value="set_no_default">Preset QUAL score-based filtering</option>
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251 <option value="set_lofreq_standard" selected="true">Preset filtering on QUAL score + coverage + strand bias (lofreq call default)</option>
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252 <option value="set_custom">Custom filter settings/combinations</option>
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253 </param>
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254 <when value="set_all_off">
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255 <param name="sig" type="hidden" value="1" />
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diff changeset
256 <param name="bonf" type="hidden" value="1" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
257 <param name="others" type="hidden" value="--no-default-filter" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
258 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
259 <when value="set_no_default">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
260 <param name="sig" type="hidden" value="0.01" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
261 <param name="bonf" type="hidden" value="dynamic" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
262 <param name="others" type="hidden" value="--no-default-filter" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
263 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
264 <when value="set_lofreq_standard">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
265 <param name="sig" type="hidden" value="0.01" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
266 <param name="bonf" type="hidden" value="dynamic" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
267 <param name="others" type="hidden" value="" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
268 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
269 <when value="set_custom">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
270 <param name="sig" type="float" value="0.01" min="0" max="1"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
271 label="Significance threshold for calls"/>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
272 <param name="bonf" type="integer" value="0" min="0"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
273 label="Bonferroni correction factor for multiple testing"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
274 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" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
275 <param name="others" type="boolean" truevalue="" falsevalue="--no-default-filter" checked="true"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
276 label="Apply default coverage and strand-bias filter?"
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
277 help="" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
278 </when>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
279 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
280 </inputs>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
281 <outputs>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
282 <data name="variants" from_work_dir="variants.vcf" format="vcf" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
283 </outputs>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
284 <tests>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
285 <test>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
286 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
287 <param name="ref_selector" value="history" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
288 <param name="ref" ftype="fasta" value="pBR322.fa" />
7
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
289 <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
290 <output name="variants" file="call-out1.vcf" lines_diff="6" />
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
291 <assert_command>
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
292 <has_text text="--sig 0.01"/>
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
293 <has_text text="--bonf dynamic"/>
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
294 <has_text text="--no-default-filter" negate="true"/>
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
295 </assert_command>
0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
296 </test>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
297 <test>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
298 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
299 <param name="ref_selector" value="history" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
300 <param name="ref" ftype="fasta" value="pBR322.fa" />
2
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
301 <conditional name="call_control">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
302 <param name="set_call_options" value="yes" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
303 </conditional>
7
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
304 <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
305 <output name="variants" file="call-out1.vcf" lines_diff="6" />
2
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
306 </test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
307 <test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
308 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
309 <param name="ref_selector" value="history" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
310 <param name="ref" ftype="fasta" value="pBR322.fa" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
311 <conditional name="call_control">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
312 <param name="set_call_options" value="yes" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
313 <section name="source_qual">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
314 <conditional name="use_src_qual">
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
315 <param name="src_qual" value="--src-qual" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
316 <param name="def_nm_q" value="40" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
317 <param name="ign_vcf" ftype="vcf" value="call-out1.vcf" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
318 </conditional>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
319 </section>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
320 </conditional>
7
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
321 <!-- lines_diff="4" should be sufficient, but https://github.com/CSB5/lofreq/issues/131 -->
4805fe3d8fda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3751719cd03b8380954e2231cf91496c863056e2
iuc
parents: 6
diff changeset
322 <output name="variants" file="call-out1.vcf" lines_diff="6" />
2
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
323 </test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
324 <test>
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
325 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
326 <param name="ref_selector" value="history" />
dfadc322b065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
iuc
parents: 0
diff changeset
327 <param name="ref" ftype="fasta" value="pBR322.fa" />
0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
328 <conditional name="filter_control">
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
329 <param name="filter_type" value="set_all_off" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
330 </conditional>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
331 <output name="variants" file="call-out2.vcf" lines_diff="4" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
332 </test>
3
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
333 <test>
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
334 <param name="reads" ftype="bam" value="indelqual-out3.bam" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
335 <param name="ref_selector" value="history" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
336 <param name="ref" ftype="fasta" value="pBR322.fa" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
337 <param name="variant_types" value="--call-indels --only-indels" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
338 <conditional name="filter_control">
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
339 <param name="filter_type" value="set_all_off" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
340 </conditional>
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
341 <output name="variants" file="indel-call-out.vcf" lines_diff="4" />
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
342 </test>
0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
343 </tests>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
344 <help><![CDATA[
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
345 lofreq call: call variants from BAM file
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
346
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
347 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
348 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
349 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
350 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
351
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
352 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
353 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
354 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
355 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
356 somatic data.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
357
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
358 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
359 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
360 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
361 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
362
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
363 **Variant calling paramters**
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
364
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
365 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
366 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
367 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
368
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
369 - Base/indel quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
370
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
371 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
372 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
373 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
374 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
375
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
376 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
377 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
378 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
379 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
380
3
3b4b2121842f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 53bf37f3bf192c4a9d14f2055f106b429cf7b5c1"
iuc
parents: 2
diff changeset
381 For doing so, you can use ``lofreq indelqual``.
0
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
382
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
383 - 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
384
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
385 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
386 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
387 correctly.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
388
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
389 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
390 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
391 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
392
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
393 - Mapping quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
394
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
395 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
396 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
397 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
398
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
399 - Source quality
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
400
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
401 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
402 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
403
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
404
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
405 **Variant filter parameters**
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
406
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
407 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
408 based on:
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
409
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
410 - 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
411 - 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
412 - 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
413
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
414 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
415 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
416 ``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
417
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
418 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
419
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
420 *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
421
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
422 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
423
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
424 - 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
425 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
426 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
427 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
428
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
429 - 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
430 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
431 genome.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
432
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
433 - 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
434
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
diff changeset
435 *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
436
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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437 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
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438 and coverage criteria
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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439
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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440 *Strictly no filtering*
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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441
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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442 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"
iuc
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443 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"
iuc
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444 output.
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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445
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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446 *Custom filter settings/combinations*
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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447
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
parents:
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448 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"
iuc
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449 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"
iuc
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450 ]]></help>
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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451 <expand macro="citations" />
31216d510164 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
iuc
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452 </tool>