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annotate FilterMutectCalls.xml @ 2:646e6943bcd2 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
author artbio
date Sun, 15 Oct 2023 12:06:24 +0000
parents c51c08cc9fcc
children
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646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
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1 <tool id="filtermutectcalls" name="gatk4 FilterMutectCalls" version="@WRAPPER_VERSION@" profile="21.01">
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c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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2 <description>Filter variants in a GATK4 Mutect2 VCF callset</description>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 #set ref_flag='--reference="reference.fa"'
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11
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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12 #if str($reference_source.reference_source_selector) == 'history'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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13 ln -s '$reference_source.reference_sequence' reference.fa &&
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14 samtools faidx reference.fa &&
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15 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
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16 #else if str($reference_source.reference_source_selector) == 'cached'
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17 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
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18 samtools faidx reference.fa &&
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19 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" &&
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20 #else
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21 #set ref_flag=''
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22 #end if
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23
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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24 #if str($input_options.input_options_selector) == 'vcf'
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25 ln -s '$input_options.unfiltered_vcf_input' input.vcf &&
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26 ln -s '$gatk_vcf_stats' input.vcf.stats &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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27 #else if str($input_options.input_options_selector) == 'vcf_bgzip'
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28 ln -s '$input_options.unfiltered_vcf_input' input.vcf.gz &&
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29 ln -s '$gatk_vcf_stats' input.vcf.gz.stats &&
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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30 gatk IndexFeatureFile --input input.vcf.gz &&
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31 #end if
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32
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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33 gatk FilterMutectCalls --QUIET $ref_flag
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34 --variant
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35 #if str($input_options.input_options_selector) == 'vcf'
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36 input.vcf
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37 #else if str($input_options.input_options_selector) == 'vcf_bgzip'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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38 input.vcf.gz
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39 #end if
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40 --output
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41 #if str($input_options.input_options_selector) == 'vcf'
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42 filtered.vcf
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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43 #else if str($input_options.input_options_selector) == 'vcf_bgzip'
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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44 filtered.vcf.gz
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45 #end if
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46 ]]>
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47 </command>
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48 <inputs>
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49 <conditional name="reference_source">
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50 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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51 <option value="cached">Locally cached</option>
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52 <option value="history" selected="true">History</option>
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53 </param>
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54 <when value="cached">
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55 <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >
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56 <options from_data_table="all_fasta" >
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57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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58 </options>
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59 </param>
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60 </when>
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61 <when value="history">
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62 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />
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63 </when>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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64 </conditional>
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65 <conditional name="input_options">
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66 <param name="input_options_selector" type="select" label="Format of input variant dataset">
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67 <option value="vcf" selected="true">vcf</option>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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68 <option value="vcf_bgzip">vcf_bgzip</option>
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69 </param>
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70 <when value="vcf">
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71 <param name="unfiltered_vcf_input" type="data" format="vcf" label="vcf input file." />
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72 </when>
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73 <when value="vcf_bgzip">
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74 <param name="unfiltered_vcf_input" type="data" format="vcf_bgzip" label="vcf_bgzip input file" />
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75 </when>
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76 </conditional>
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77 <param format="tabular" name="gatk_vcf_stats" type="data" label="gatk vcf stats" help="this stats file is generated by the Mutect2 tool"/>
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78 </inputs>
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79 <outputs>
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80 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: Filtered vcf" from_work_dir="filtered.vcf" >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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81 <filter>input_options['input_options_selector'] == 'vcf'</filter>
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82 </data>
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83 <data format="tabular" name="output_vcf_stats" label="${tool.name}: Filtered vcf statistics" from_work_dir="filtered.vcf.filteringStats.tsv" >
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84 <filter>input_options['input_options_selector'] == 'vcf'</filter>
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85 </data>
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86 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: Filtered vcf (bgzip)" from_work_dir="filtered.vcf.gz" >
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87 <filter>input_options['input_options_selector'] == 'vcf_bgzip'</filter>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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88 </data>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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89 <data format="tabular" name="output_vcf_bgzip_stats" label="${tool.name}: Filtered vcf (bgzip) statistics" from_work_dir="filtered.vcf.gz.filteringStats.tsv" >
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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90 <filter>input_options['input_options_selector'] == 'vcf_bgzip'</filter>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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91 </data>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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92 </outputs>
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93 <tests>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
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94 <test expect_num_outputs="2">
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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95 <param name="reference_source_selector" value="history" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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96 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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97 <conditional name="input_options">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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98 <param name="unfiltered_vcf_input" ftype="vcf" value="Mutect2-out1.vcf" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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99 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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100 <param name="gatk_vcf_stats" ftype="tabular" value="Mutect2-out1.vcf.stats" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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101 <output name="output_vcf" file="filtered_Mutect2-out1.vcf" lines_diff="2" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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102 <output name="output_vcf_stats" file="filtered_Mutect2-out1_stats.tsv" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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103 </test>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
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104 <test expect_num_outputs="2">
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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105 <param name="reference_source_selector" value="history" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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106 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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107 <conditional name="input_options">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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108 <param name="input_options_selector" value="vcf_bgzip" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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109 <param name="unfiltered_vcf_input" ftype="vcf_bgzip" value="Mutect2-out6.vcf_bgzip" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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110 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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111 <param name="gatk_vcf_stats" ftype="tabular" value="Mutect2-out6.vcf_bgzip.stats" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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112 <output name="output_vcf" file="filtered_Mutect2-out6.vcf_bgzip" compare="sim_size" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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113 <output name="output_vcf_stats" file="filtered_Mutect2-out6_stats.tsv" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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114 </test>
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
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115 <test expect_num_outputs="2">
0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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116 <param name="reference_source_selector" value="history" />
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117 <param name="reference_sequence" ftype="fasta" value="chr20.fa" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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118 <conditional name="input_options">
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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119 <param name="input_options_selector" value="vcf" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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120 <param name="unfiltered_vcf_input" ftype="vcf" value="Mutect2-out6.vcf" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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121 </conditional>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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122 <param name="gatk_vcf_stats" ftype="tabular" value="Mutect2-out6.vcf_bgzip.stats" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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123 <output name="output_vcf" file="filtered_Mutect2-out6.vcf" lines_diff="2" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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124 <output name="output_vcf_stats" file="filtered_Mutect2-out6_stats.tsv" />
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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125 </test>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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126 </tests>
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127 <help><![CDATA[
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128 Usage examples
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129 ~~~~~~~~~~~~~~
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130
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131
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132 ::
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133
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134 gatk FilterMutectCalls \\
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135
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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136 -R reference.fasta \\
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137
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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138 -V somatic.vcf.gz \\
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139
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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140 --contamination-table contamination.table \\
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141
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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142 --tumor-segmentation segments.tsv \\
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143
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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144 -O filtered.vcf.gz
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145
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146
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147 When running on unfiltered output of Mutect2 in --mitochondria mode, setting the advanced
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148 option --autosomal-coverage argument (default 0) activates a recommended filter against
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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149 likely erroneously mapped NuMTs (nuclear mitochondrial DNA segments -- https://en.wikipedia.org/wiki/NUMT).
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150 For the value, provide the median coverage expected in autosomal regions with coverage.
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151
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152
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153 Usage
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154 ~~~~~
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155
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156
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157 ::
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158
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159 USAGE: FilterMutectCalls [arguments]
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160
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161 Filter somatic SNVs and indels called by Mutect2
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162 Version:4.1.7.0
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163
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164
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165 Required Arguments:
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166
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167 --output,-O:String The output filtered VCF file Required.
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168
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169 --reference,-R:GATKPathSpecifier
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170 Reference sequence file Required.
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171
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172 --variant,-V:String A VCF file containing variants Required.
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173
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174
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175 Optional Arguments:
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176
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177 --add-output-sam-program-record,-add-output-sam-program-record:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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178 If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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179 values: {true, false}
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180
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181 --add-output-vcf-command-line,-add-output-vcf-command-line:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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182 If true, adds a command line header line to created VCF files. Default value: true.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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183 Possible values: {true, false}
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184
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185 --arguments_file:File read one or more arguments files and add them to the command line This argument may be
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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diff changeset
186 specified 0 or more times. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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187
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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188 --cloud-index-prefetch-buffer,-CIPB:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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189 Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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190 cloudPrefetchBuffer if unset. Default value: -1.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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191
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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192 --cloud-prefetch-buffer,-CPB:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
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193 Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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diff changeset
194
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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195 --contamination-estimate:Double
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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196 Estimate of contamination. Default value: 0.0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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197
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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198 --contamination-table:File Tables containing contamination information. This argument may be specified 0 or more
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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199 times. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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200
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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201 --create-output-bam-index,-OBI:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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202 If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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203 value: true. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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204
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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205 --create-output-bam-md5,-OBM:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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diff changeset
206 If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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207 Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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208
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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209 --create-output-variant-index,-OVI:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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210 If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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211 true. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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212
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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213 --create-output-variant-md5,-OVM:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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214 If true, create a a MD5 digest any VCF file created. Default value: false. Possible
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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215 values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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216
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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217 --disable-bam-index-caching,-DBIC:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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218 If true, don't cache bam indexes, this will reduce memory requirements but may harm
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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219 performance if many intervals are specified. Caching is automatically disabled if there
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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220 are no intervals specified. Default value: false. Possible values: {true, false}
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221
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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222 --disable-read-filter,-DF:String
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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223 Read filters to be disabled before analysis This argument may be specified 0 or more
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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224 times. Default value: null. Possible Values: {WellformedReadFilter}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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225
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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226 --disable-sequence-dictionary-validation,-disable-sequence-dictionary-validation:Boolean
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227 If specified, do not check the sequence dictionaries from our inputs for compatibility.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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228 Use at your own risk! Default value: false. Possible values: {true, false}
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229
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230 --distance-on-haplotype:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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231 On second filtering pass, variants with same PGT and PID tags as a filtered variant within
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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232 this distance are filtered. Default value: 100.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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233
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234 --exclude-intervals,-XL:StringOne or more genomic intervals to exclude from processing This argument may be specified 0
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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235 or more times. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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236
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237 --f-score-beta:Double F score beta, the relative weight of recall to precision, used if OPTIMAL_F_SCORE strategy
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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238 is chosen Default value: 1.0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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239
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240 --false-discovery-rate:Double Maximum false discovery rate allowed if FALSE_DISCOVERY_RATE threshold strategy is chosen
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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241 Default value: 0.05.
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242
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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243 --filtering-stats:String The output filtering stats file Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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244
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245 --gatk-config-file:String A configuration file to use with the GATK. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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246
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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247 --gcs-max-retries,-gcs-retries:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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248 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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249 connection Default value: 20.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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250
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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251 --gcs-project-for-requester-pays:String
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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252 Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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253 accessed. Default value: .
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254
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255 --help,-h:Boolean display the help message Default value: false. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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256
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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257 --initial-threshold:Double Initial artifact probability threshold used in first iteration Default value: 0.1.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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258
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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259 --input,-I:String BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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260 Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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261
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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262 --interval-exclusion-padding,-ixp:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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263 Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
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diff changeset
264
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
265 --interval-merging-rule,-imr:IntervalMergingRule
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
266 Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
267 OVERLAPPING_ONLY}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
268
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
269 --interval-padding,-ip:IntegerAmount of padding (in bp) to add to each interval you are including. Default value: 0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
270
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
271 --interval-set-rule,-isr:IntervalSetRule
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
272 Set merging approach to use for combining interval inputs Default value: UNION. Possible
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
273 values: {UNION, INTERSECTION}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
274
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
275 --intervals,-L:String One or more genomic intervals over which to operate This argument may be specified 0 or
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
276 more times. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
277
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
278 --lenient,-LE:Boolean Lenient processing of VCF files Default value: false. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
279
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
280 --log-artifact-prior:Double Initial ln prior probability that a called site is not a technical artifact Default
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
281 value: -2.302585092994046.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
282
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
283 --log-indel-prior:Double Initial ln prior probability that a site has a somatic indel Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
284 -16.11809565095832.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
285
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
286 --log-snv-prior:Double Initial ln prior probability that a site has a somatic SNV Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
287 -13.815510557964275.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
288
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
289 --long-indel-length:Integer Indels of this length or greater are treated specially by the mapping quality filter.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
290 Default value: 5.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
291
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
292 --max-alt-allele-count:IntegerMaximum alt alleles per site. Default value: 1.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
293
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
294 --max-events-in-region:IntegerMaximum events in a single assembly region. Filter all variants if exceeded. Default
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
295 value: 2.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
296
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
297 --max-median-fragment-length-difference:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
298 Maximum difference between median alt and ref fragment lengths Default value: 10000.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
299
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
300 --max-n-ratio:Double Maximum fraction of non-ref bases in the pileup that are N (unknown) Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
301 Infinity.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
302
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
303 --min-allele-fraction:Double Minimum allele fraction required Default value: 0.0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
304
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
305 --min-median-base-quality:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
306 Minimum median base quality of alt reads Default value: 20.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
307
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
308 --min-median-mapping-quality:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
309 Minimum median mapping quality of alt reads Default value: 30.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
310
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
311 --min-median-read-position:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
312 Minimum median distance of variants from the end of reads Default value: 1.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
313
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
314 --min-reads-per-strand:IntegerMinimum alt reads required on both forward and reverse strands Default value: 0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
315
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
316 --min-slippage-length:Integer Minimum number of reference bases in an STR to suspect polymerase slippage Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
317 8.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
318
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
319 --mitochondria-mode:Boolean Set filters to mitochondrial defaults Default value: false. Possible values: {true,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
320 false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
321
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
322 --normal-p-value-threshold:Double
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
323 P value threshold for normal artifact filter Default value: 0.001.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
324
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
325 --orientation-bias-artifact-priors,-ob-priors:File
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
326 One or more .tar.gz files containing tables of prior artifact probabilities for the read
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
327 orientation filter model, one table per tumor sample This argument may be specified 0 or
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
328 more times. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
329
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
330 --pcr-slippage-rate:Double The frequency of polymerase slippage in contexts where it is suspected Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
331 0.1.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
332
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
333 --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
334 values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
335
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
336 --read-filter,-RF:String Read filters to be applied before analysis This argument may be specified 0 or more
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
337 times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
338 AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
339 FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
340 HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
341 MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
342 MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
343 MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
344 MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
345 NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
346 NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
347 NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
348 NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
349 OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
350 PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
351 ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
352 ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter, ReadNameReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
353 ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter, SeqIsStoredReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
354 SoftClippedReadFilter, ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
355 WellformedReadFilter}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
356
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
357 --read-index,-read-index:String
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
358 Indices to use for the read inputs. If specified, an index must be provided for every read
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
359 input and in the same order as the read inputs. If this argument is not specified, the
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
360 path to the index for each input will be inferred automatically. This argument may be
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
361 specified 0 or more times. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
362
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
363 --read-validation-stringency,-VS:ValidationStringency
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
364 Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
365 stringency value SILENT can improve performance when processing a BAM file in which
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
366 variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
367 value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
368
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
369 --seconds-between-progress-updates,-seconds-between-progress-updates:Double
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
370 Output traversal statistics every time this many seconds elapse Default value: 10.0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
371
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
372 --sequence-dictionary,-sequence-dictionary:String
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
373 Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
374 .dict file. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
375
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
376 --sites-only-vcf-output:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
377 If true, don't emit genotype fields when writing vcf file output. Default value: false.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
378 Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
379
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
380 --stats:String The Mutect stats file output by Mutect2 Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
381
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
382 --threshold-strategy:Strategy The method for optimizing the posterior probability threshold Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
383 OPTIMAL_F_SCORE. Possible values: {CONSTANT, FALSE_DISCOVERY_RATE, OPTIMAL_F_SCORE}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
384
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
385 --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
386
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
387 --tumor-segmentation:File Tables containing tumor segments' minor allele fractions for germline hets emitted by
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
388 CalculateContamination This argument may be specified 0 or more times. Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
389 null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
390
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
391 --unique-alt-read-count,-unique:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
392 Minimum unique (i.e. deduplicated) reads supporting the alternate allele Default value:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
393 0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
394
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
395 --use-jdk-deflater,-jdk-deflater:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
396 Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
397 Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
398
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
399 --use-jdk-inflater,-jdk-inflater:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
400 Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
401 Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
402
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
403 --verbosity,-verbosity:LogLevel
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
404 Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
405 INFO, DEBUG}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
406
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
407 --version:Boolean display the version number for this tool Default value: false. Possible values: {true,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
408 false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
409
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
410
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
411 Advanced Arguments:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
412
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
413 --disable-tool-default-read-filters,-disable-tool-default-read-filters:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
414 Disable all tool default read filters (WARNING: many tools will not function correctly
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
415 without their default read filters on) Default value: false. Possible values: {true,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
416 false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
417
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
418 --showHidden,-showHidden:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
419 display hidden arguments Default value: false. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
420
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
421 Conditional Arguments for readFilter:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
422
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
423 Valid only if "AmbiguousBaseReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
424 --ambig-filter-bases:Integer Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
425 overrides threshold fraction. Default value: null. Cannot be used in conjuction with
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
426 argument(s) maxAmbiguousBaseFraction
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
427
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
428 --ambig-filter-frac:Double Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjuction
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
429 with argument(s) maxAmbiguousBases
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
430
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
431 Valid only if "FragmentLengthReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
432 --max-fragment-length:Integer Maximum length of fragment (insert size) Default value: 1000000.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
433
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
434 --min-fragment-length:Integer Minimum length of fragment (insert size) Default value: 0.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
435
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
436 Valid only if "IntervalOverlapReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
437 --keep-intervals:String One or more genomic intervals to keep This argument must be specified at least once.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
438 Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
439
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
440 Valid only if "LibraryReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
441 --library,-library:String Name of the library to keep This argument must be specified at least once. Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
442
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
443 Valid only if "MappingQualityReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
444 --maximum-mapping-quality:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
445 Maximum mapping quality to keep (inclusive) Default value: null.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
446
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
447 --minimum-mapping-quality:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
448 Minimum mapping quality to keep (inclusive) Default value: 10.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
449
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
450 Valid only if "MateDistantReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
451 --mate-too-distant-length:Integer
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
452 Minimum start location difference at which mapped mates are considered distant Default
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
453 value: 1000.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
454
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
455 Valid only if "OverclippedReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
456 --dont-require-soft-clips-both-ends:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
457 Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
458 both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
459 block Default value: false. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
460
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
461 --filter-too-short:Integer Minimum number of aligned bases Default value: 30.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
462
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
463 Valid only if "PlatformReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
464 --platform-filter-name:String Platform attribute (PL) to match This argument must be specified at least once. Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
465
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
466 Valid only if "PlatformUnitReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
467 --black-listed-lanes:String Platform unit (PU) to filter out This argument must be specified at least once. Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
468
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
469 Valid only if "ReadGroupBlackListReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
470 --read-group-black-list:StringA read group filter expression in the form "attribute:value", where "attribute" is a two
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
471 character read group attribute such as "RG" or "PU". This argument must be specified at
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
472 least once. Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
473
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
474 Valid only if "ReadGroupReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
475 --keep-read-group:String The name of the read group to keep Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
476
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
477 Valid only if "ReadLengthReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
478 --max-read-length:Integer Keep only reads with length at most equal to the specified value Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
479
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
480 --min-read-length:Integer Keep only reads with length at least equal to the specified value Default value: 1.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
481
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
482 Valid only if "ReadNameReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
483 --read-name:String Keep only reads with this read name Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
484
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
485 Valid only if "ReadStrandFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
486 --keep-reverse-strand-only:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
487 Keep only reads on the reverse strand Required. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
488
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
489 Valid only if "SampleReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
490 --sample,-sample:String The name of the sample(s) to keep, filtering out all others This argument must be
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
491 specified at least once. Required.
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
492
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
493 Valid only if "SoftClippedReadFilter" is specified:
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
494 --invert-soft-clip-ratio-filter:Boolean
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
495 Inverts the results from this filter, causing all variants that would pass to fail and
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
496 visa-versa. Default value: false. Possible values: {true, false}
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
497
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
498 --soft-clipped-leading-trailing-ratio:Double
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
499 Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
500 in read for read to be filtered. Default value: null. Cannot be used in conjuction with
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
501 argument(s) minimumSoftClippedRatio
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
502
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
503 --soft-clipped-ratio-threshold:Double
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
504 Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
505 read for read to be filtered. Default value: null. Cannot be used in conjuction with
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
506 argument(s) minimumLeadingTrailingSoftClippedRatio
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
507
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
508
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
509 ]]></help>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
510 <citations>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
511 <expand macro="citations"/>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
512 </citations>
c51c08cc9fcc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit 408454e8d10befcc76f38ab446091778537d4f31"
artbio
parents:
diff changeset
513 </tool>