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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 commit 30797e29f13902f17652cf35585e52b363c28a31
author iuc
date Tue, 03 Feb 2026 18:50:29 +0000
parents 91d37702c47b
children
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7:91d37702c47b 8:55e8a08e39e1
1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@WRAPPER_VERSION@+galaxy1" profile="18.05"> 1 <tool id="gatk4_mutect2" name="GATK4 Mutect2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description> 2 <description>- Call somatic SNVs and indels via local assembly of haplotypes</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
9 <![CDATA[ 9 <![CDATA[
10 #include source=$set_sections# 10 #include source=$set_sections#
11 #include source=$pre_gatk_excl_ints_chth# 11 #include source=$pre_gatk_excl_ints_chth#
12 #include source=$pre_gatk_ints_chth# 12 #include source=$pre_gatk_ints_chth#
13 13
14 #set ref_flag='--reference="reference.fa"' 14 #set ref_flag='-R reference.fa'
15 15
16 #if str($reference_source.reference_source_selector) == 'history' 16 #if str($reference_source.reference_source_selector) == 'history'
17 ln -s '$reference_source.reference_sequence' reference.fa && 17 ln -s '$reference_source.reference_sequence' reference.fa &&
18 samtools faidx reference.fa && 18 samtools faidx reference.fa &&
19 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && 19 gatk CreateSequenceDictionary -R reference.fa -O reference.dict &&
20 #else if str($reference_source.reference_source_selector) == 'cached' 20 #else if str($reference_source.reference_source_selector) == 'cached'
21 ln -s '$reference_source.reference_sequence.fields.path' reference.fa && 21 ln -s '$reference_source.reference_sequence.fields.path' reference.fa &&
22 samtools faidx reference.fa && 22 samtools faidx reference.fa &&
23 gatk CreateSequenceDictionary --REFERENCE="reference.fa" --OUTPUT="reference.dict" && 23 gatk CreateSequenceDictionary -R reference.fa -O reference.dict &&
24 #else 24 #else
25 #set ref_flag='' 25 #set ref_flag=''
26 #end if 26 #end if
27 27
28 #if str($mode.mode_parameters) == 'tumor_only' 28 #if str($mode.mode_parameters) == 'tumor_only'
42 #if str($outputs.debug_bam) == 'yes' 42 #if str($outputs.debug_bam) == 'yes'
43 ln -s '$bam_output' debug.bam && 43 ln -s '$bam_output' debug.bam &&
44 #end if 44 #end if
45 #end if 45 #end if
46 46
47 gatk GetSampleName --input="tumor.bam" --output="samplename.txt" && 47 gatk GetSampleName -I tumor.bam -O samplename.txt &&
48 sample=`cat samplename.txt | sed 's/"//g'` && 48 sample=`cat samplename.txt | sed 's/"//g'` &&
49 49
50 #if str($optional.optional_parameters) == 'yes' 50 #if str($optional.optional_parameters) == 'yes'
51 #if $optional.panel_of_normals 51 #if $optional.panel_of_normals
52 #set datatype = $optional.panel_of_normals.datatype 52 #set datatype = $optional.panel_of_normals.datatype
102 --panel-of-normals panel_of_normals.vcf 102 --panel-of-normals panel_of_normals.vcf
103 #end if 103 #end if
104 #end if 104 #end if
105 105
106 #if $optional.pedigree 106 #if $optional.pedigree
107 --pedigree="$optional.pedigree" 107 --pedigree "$optional.pedigree"
108 #end if 108 #end if
109 109
110 #if $optional.germline_resource 110 #if $optional.germline_resource
111 #if $optional.germline_resource.is_of_type("vcf_bgzip") 111 #if $optional.germline_resource.is_of_type("vcf_bgzip")
112 --germline-resource germline_resource.vcf.gz 112 --germline-resource germline_resource.vcf.gz
115 #end if 115 #end if
116 #end if 116 #end if
117 117
118 #if $optional.annotation 118 #if $optional.annotation
119 #for $annot in str($optional.annotation).split(',') 119 #for $annot in str($optional.annotation).split(',')
120 --annotation="$annot" 120 --annotation "$annot"
121 #end for 121 #end for
122 #end if 122 #end if
123 123
124 #if $optional.annotation_group 124 #if $optional.annotation_group
125 #for $annot in str($optional.annotation_group).split(',') 125 #for $annot in str($optional.annotation_group).split(',')
126 --annotation-group="$annot" 126 --annotation-group "$annot"
127 #end for 127 #end for
128 #end if 128 #end if
129 129
130 #if $optional.annotations_to_exclude 130 #if $optional.annotations_to_exclude
131 #for $annot in str($optional.annotations_to_exclude).split(',') 131 #for $annot in str($optional.annotations_to_exclude).split(',')
132 --annotations-to-exclude="$annot" 132 --annotations-to-exclude "$annot"
133 #end for 133 #end for
134 #end if 134 #end if
135 135
136 #if $optional.founder_id 136 #if $optional.founder_id
137 --founder-id="$optional.founder_id" 137 --founder-id "$optional.founder_id"
138 #end if 138 #end if
139 139
140 #if $optional.normal_sample 140 #if $optional.normal_sample
141 --normal-sample="$optional.normal_sample" 141 --normal-sample "$optional.normal_sample"
142 #end if 142 #end if
143 143
144 #if $optional.alleles 144 #if $optional.alleles
145 --alleles alleles.vcf 145 --alleles alleles.vcf
146 #end if 146 #end if
147 147
148 #if $optional.f1r2_max_depth: 148 #if $optional.f1r2_max_depth:
149 --f1r2-max-depth="$optional.f1r2_max_depth" 149 --f1r2-max-depth "$optional.f1r2_max_depth"
150 #end if 150 #end if
151 151
152 #if $optional.f1r2_max_depth: 152 #if $optional.f1r2_median_mq:
153 --f1r2-median-mq="$optional.f1r2_median_mq" 153 --f1r2-median-mq "$optional.f1r2_median_mq"
154 #end if 154 #end if
155 155
156 #if $optional.f1r2_max_depth: 156 #if $optional.f1r2_min_bq:
157 --f1r2-min-bq="$optional.f1r2_min_bq" 157 --f1r2-min-bq "$optional.f1r2_min_bq"
158 #end if 158 #end if
159 159
160 #if $optional.interval_merging_rule: 160 #if $optional.interval_merging_rule:
161 --interval-merging-rule="$optional.interval_merging_rule" 161 --interval-merging-rule "$optional.interval_merging_rule"
162 #end if 162 #end if
163 163
164 #if $optional.interval_set_rule: 164 #if $optional.interval_set_rule:
165 --interval-set-rule="$optional.interval_set_rule" 165 --interval-set-rule "$optional.interval_set_rule"
166 #end if 166 #end if
167 167
168 #if $optional.pcr_indel_qual: 168 #if $optional.pcr_indel_qual:
169 --pcr-indel-qual="$optional.pcr_indel_qual" 169 --pcr-indel-qual "$optional.pcr_indel_qual"
170 #end if 170 #end if
171 171
172 #if $optional.pcr_snv_qual: 172 #if $optional.pcr_snv_qual:
173 --pcr-snv-qual="$optional.pcr_snv_qual" 173 --pcr-snv-qual "$optional.pcr_snv_qual"
174 #end if 174 #end if
175 175
176 #if $optional.read_filter 176 #if $optional.read_filter
177 #for $filter in str($optional.read_filter).split(',') 177 #for $filter in str($optional.read_filter).split(',')
178 --read-filter="$filter" 178 --read-filter "$filter"
179 #end for 179 #end for
180 #end if 180 #end if
181 181
182 #if $optional.disable_read_filter 182 #if $optional.disable_read_filter
183 #for $filter in str($optional.disable_read_filter).split(',') 183 #for $filter in str($optional.disable_read_filter).split(',')
184 --disable-read-filter="$filter" 184 --disable-read-filter "$filter"
185 #end for 185 #end for
186 #end if 186 #end if
187 187
188 --base-quality-score-threshold="$optional.base_quality_score_threshold" 188 --base-quality-score-threshold "$optional.base_quality_score_threshold"
189 --af-of-alleles-not-in-resource="$optional.af_of_alleles_not_in_resource" 189 --af-of-alleles-not-in-resource "$optional.af_of_alleles_not_in_resource"
190 --downsampling-stride="$optional.downsampling_stride" 190 --downsampling-stride "$optional.downsampling_stride"
191 --gcs-max-retries="$optional.gcs_max_retries" 191 --gcs-max-retries "$optional.gcs_max_retries"
192 --initial-tumor-lod="$optional.initial_tumor_lod" 192 --initial-tumor-lod "$optional.initial_tumor_lod"
193 --max-population-af="$optional.max_population_af" 193 --max-population-af "$optional.max_population_af"
194 --max-reads-per-alignment-start="$optional.max_reads_per_alignment_start" 194 --max-reads-per-alignment-start "$optional.max_reads_per_alignment_start"
195 --min-base-quality-score="$optional.min_base_quality_score" 195 --min-base-quality-score "$optional.min_base_quality_score"
196 --native-pair-hmm-threads="\${GALAXY_SLOTS:-1}" 196 --native-pair-hmm-threads "\${GALAXY_SLOTS:-1}"
197 --normal-lod="$optional.normal_lod" 197 --normal-lod "$optional.normal_lod"
198 --read-validation-stringency="$optional.read_validation_stringency" 198 --read-validation-stringency "$optional.read_validation_stringency"
199 --tumor-lod-to-emit="$optional.tumor_lod_to_emit" 199 --tumor-lod-to-emit "$optional.tumor_lod_to_emit"
200 --verbosity="ERROR" 200 --verbosity "ERROR"
201 $optional.lenient 201 $optional.lenient
202 $optional.annotate_with_num_discovered_alleles 202 $optional.annotate_with_num_discovered_alleles
203 $optional.add_output_sam_program_record 203 $optional.add_output_sam_program_record
204 $optional.disable_bam_index_caching 204 $optional.disable_bam_index_caching
205 $optional.disable_sequence_dictionary_validation 205 $optional.disable_sequence_dictionary_validation
217 ## ADVANCED PARAMETERS ## 217 ## ADVANCED PARAMETERS ##
218 218
219 #if str($advanced.advanced_parameters) == 'yes' 219 #if str($advanced.advanced_parameters) == 'yes'
220 220
221 #if $advanced.kmer_size 221 #if $advanced.kmer_size
222 --kmer-size="$advanced.kmer_size" 222 --kmer-size "$advanced.kmer_size"
223 #end if 223 #end if
224 224
225 #if $advanced.gvcf_lod_band 225 #if $advanced.gvcf_lod_band
226 --gvcf-lod-band="$advanced.gvcf_lod_band" 226 --gvcf-lod-band "$advanced.gvcf_lod_band"
227 #end if 227 #end if
228 228
229 #if $advanced.emit_ref_confidence 229 #if $advanced.emit_ref_confidence
230 --emit-ref-confidence="$advanced.emit_ref_confidence" 230 --emit-ref-confidence "$advanced.emit_ref_confidence"
231 #end if 231 #end if
232 232
233 #if $advanced.max_unpruned_variants 233 #if $advanced.max_unpruned_variants
234 --max-unpruned-variants="$advanced.max_unpruned_variants" 234 --max-unpruned-variants "$advanced.max_unpruned_variants"
235 #end if 235 #end if
236 --allele-informative-reads-overlap-margin="$advanced.allele_informative_reads_overlap_margin" 236 --allele-informative-reads-overlap-margin "$advanced.allele_informative_reads_overlap_margin"
237 --active-probability-threshold="$advanced.active_probability_threshold" 237 --active-probability-threshold "$advanced.active_probability_threshold"
238 --assembly-region-padding="$advanced.assembly_region_padding" 238 --assembly-region-padding "$advanced.assembly_region_padding"
239 --bam-writer-type="$advanced.bam_writer_type" 239 --bam-writer-type "$advanced.bam_writer_type"
240 --max-assembly-region-size="$advanced.max_assembly_region_size" 240 --max-assembly-region-size "$advanced.max_assembly_region_size"
241 --max-mnp-distance="$advanced.max_mnp_distance" 241 --max-mnp-distance "$advanced.max_mnp_distance"
242 --max-num-haplotypes-in-population="$advanced.max_num_haplotypes_in_population" 242 --max-num-haplotypes-in-population "$advanced.max_num_haplotypes_in_population"
243 --max-prob-propagation-distance="$advanced.max_prob_propagation_distance" 243 --max-prob-propagation-distance "$advanced.max_prob_propagation_distance"
244 --max-suspicious-reads-per-alignment-start="$advanced.max_suspicious_reads_per_alignment_start" 244 --max-suspicious-reads-per-alignment-start "$advanced.max_suspicious_reads_per_alignment_start"
245 --min-assembly-region-size="$advanced.min_assembly_region_size" 245 --min-assembly-region-size "$advanced.min_assembly_region_size"
246 --min-dangling-branch-length="$advanced.min_dangling_branch_length" 246 --min-dangling-branch-length "$advanced.min_dangling_branch_length"
247 --min-pruning="$advanced.min_pruning" 247 --min-pruning "$advanced.min_pruning"
248 --minimum-allele-fraction="$advanced.minimum_allele_fraction" 248 --minimum-allele-fraction "$advanced.minimum_allele_fraction"
249 --num-pruning-samples="$advanced.num_pruning_samples" 249 --num-pruning-samples "$advanced.num_pruning_samples"
250 --pair-hmm-gap-continuation-penalty="$advanced.pair_hmm_gap_continuation_penalty" 250 --pair-hmm-gap-continuation-penalty "$advanced.pair_hmm_gap_continuation_penalty"
251 --callable-depth="$advanced.callable_depth" 251 --callable-depth "$advanced.callable_depth"
252 --pair-hmm-implementation="$advanced.pair_hmm_implementation" 252 --pair-hmm-implementation "$advanced.pair_hmm_implementation"
253 --pcr-indel-model="$advanced.pcr_indel_model" 253 --pcr-indel-model "$advanced.pcr_indel_model"
254 --phred-scaled-global-read-mismapping-rate="$advanced.phred_scaled_global_read_mismapping_rate" 254 --phred-scaled-global-read-mismapping-rate "$advanced.phred_scaled_global_read_mismapping_rate"
255 --pruning-lod-threshold="$advanced.pruning_lod_threshold" 255 --pruning-lod-threshold "$advanced.pruning_lod_threshold"
256 --smith-waterman="$advanced.smith_waterman" 256 --smith-waterman "$advanced.smith_waterman"
257 $advanced.allow_non_unique_kmers_in_ref 257 $advanced.allow_non_unique_kmers_in_ref
258 $advanced.disable_adaptive_pruning 258 $advanced.disable_adaptive_pruning
259 $advanced.disable_tool_default_annotations 259 $advanced.disable_tool_default_annotations
260 $advanced.disable_tool_default_read_filters 260 $advanced.disable_tool_default_read_filters
261 $advanced.dont_increase_kmer_sizes_for_cycles 261 $advanced.dont_increase_kmer_sizes_for_cycles
273 273
274 ## ADDITIONAL OUTPUT PARAMETERS ## 274 ## ADDITIONAL OUTPUT PARAMETERS ##
275 275
276 #if str($outputs.output_parameters) == 'yes' 276 #if str($outputs.output_parameters) == 'yes'
277 #if str($outputs.debug_assembly) == 'yes' 277 #if str($outputs.debug_assembly) == 'yes'
278 --assembly-region-out="assembly-region.tab" 278 --assembly-region-out "assembly-region.tab"
279 #end if 279 #end if
280 #if str($outputs.debug_bam) == 'yes' 280 #if str($outputs.debug_bam) == 'yes'
281 --bam-output="debug.bam" 281 --bam-output "debug.bam"
282 #end if 282 #end if
283 #end if 283 #end if
284 284
285 #include source=$gatk_excl_ints_chth# 285 #include source=$gatk_excl_ints_chth#
286 #include source=$gatk_ints_chth# 286 #include source=$gatk_ints_chth#
499 <param name="read_validation_stringency" argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded."> 499 <param name="read_validation_stringency" argument="--read-validation-stringency" type="select" optional="true" label="Read Validation Stringency" help="Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.">
500 <option selected="true" value="SILENT">Silent</option> 500 <option selected="true" value="SILENT">Silent</option>
501 <option value="STRICT">Strict</option> 501 <option value="STRICT">Strict</option>
502 <option value="LENIENT">Lenient</option> 502 <option value="LENIENT">Lenient</option>
503 </param> 503 </param>
504 <param name="sites_only_vcf_output" argument="--sites-only-vcf-output" type="boolean" truevalue="--sites-only-vcf-output" falsevalue="" optional="true" checked="false" label="Sites Only Vcf Output" help="If true, don&amp;apos;t emit genotype fields when writing vcf file output."/>
505 <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/> 504 <param name="tumor_lod_to_emit" argument="--tumor-lod-to-emit" type="float" optional="true" value="3.0" label="Tumor Lod To Emit" help="LOD threshold to emit tumor variant to VCF."/>
506 </when> 505 </when>
507 <when value="no" /> 506 <when value="no" />
508 </conditional> 507 </conditional>
509 <conditional name="advanced"> 508 <conditional name="advanced">
596 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output"> 595 <data format="bam" name="bam_output" label="${tool.name} on ${on_string}: Debug BAM output">
597 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter> 596 <filter>str(outputs['output_parameters']) == 'yes' and outputs['debug_bam']</filter>
598 </data> 597 </data>
599 </outputs> 598 </outputs>
600 <tests> 599 <tests>
601 <test> 600 <test expect_num_outputs='1'>
602 <conditional name="mode"> 601 <conditional name="mode">
603 <param name="mode_parameters" value="tumor_only"/> 602 <param name="mode_parameters" value="tumor_only"/>
604 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" /> 603 <param name="tumor" ftype="bam" value="Mutect2-in1.bam" />
605 </conditional> 604 </conditional>
606 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 605 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
607 <param name="gzipped_output" value="false" /> 606 <param name="gzipped_output" value="false" />
608 <param name="reference_source_selector" value="history" /> 607 <param name="reference_source_selector" value="history" />
609 <param name="optional_parameters" value="no" /> 608 <param name="optional_parameters" value="no" />
610 <param name="advanced_parameters" value="no" /> 609 <param name="advanced_parameters" value="no" />
611 <param name="output_parameters" value="no" /> 610 <param name="output_parameters" value="no" />
612 <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="2" /> 611 <output name="output_vcf" file="Mutect2-out1.vcf" lines_diff="48">
612 <assert_contents>
613 <has_n_lines n="90"/>
614 </assert_contents>
615 </output>
613 </test> 616 </test>
614 <test> 617 <test expect_num_outputs='1'>
615 <conditional name="mode"> 618 <conditional name="mode">
616 <param name="mode_parameters" value="tumor_only"/> 619 <param name="mode_parameters" value="tumor_only"/>
617 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" /> 620 <param name="tumor" ftype="bam" value="Mutect2-in2.bam" />
618 </conditional> 621 </conditional>
619 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 622 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
620 <param name="gzipped_output" value="false" /> 623 <param name="gzipped_output" value="false" />
621 <param name="reference_source_selector" value="history" /> 624 <param name="reference_source_selector" value="history" />
622 <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" /> 625 <param name="read_filter" value="AmbiguousBaseReadFilter,FirstOfPairReadFilter,GoodCigarReadFilter" />
623 <param name="seqdict_source" value="history" /> 626 <param name="seqdict_source_selector" value="history" />
624 <param name="seqdict_sequence" value="Mutect2-in2.dict" /> 627 <param name="seqdict_sequence" value="Mutect2-in2.dict" />
625 <param name="optional_parameters" value="no" /> 628 <param name="optional_parameters" value="no" />
626 <param name="advanced_parameters" value="no" /> 629 <param name="advanced_parameters" value="no" />
627 <param name="output_parameters" value="no" /> 630 <param name="output_parameters" value="no" />
628 <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="2" /> 631 <output name="output_vcf" file="Mutect2-out2.vcf" lines_diff="48">
632 <assert_contents>
633 <has_n_lines n="128"/>
634 </assert_contents>
635 </output>
629 </test> 636 </test>
630 <test> 637 <test expect_num_outputs='1'>
631 <conditional name="mode"> 638 <conditional name="mode">
632 <param name="mode_parameters" value="tumor_only"/> 639 <param name="mode_parameters" value="tumor_only"/>
633 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" /> 640 <param name="tumor" ftype="bam" value="Mutect2-in3.bam" />
634 </conditional> 641 </conditional>
635 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 642 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
638 <param name="optional_parameters" value="yes" /> 645 <param name="optional_parameters" value="yes" />
639 <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" /> 646 <param name="annotation" value="StrandBiasBySample,BaseQualityHistogram,OrientationBiasReadCounts" />
640 <param name="annotation_group" value="StandardMutectAnnotation" /> 647 <param name="annotation_group" value="StandardMutectAnnotation" />
641 <param name="advanced_parameters" value="no" /> 648 <param name="advanced_parameters" value="no" />
642 <param name="output_parameters" value="no" /> 649 <param name="output_parameters" value="no" />
643 <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="2" /> 650 <output name="output_vcf" file="Mutect2-out3.vcf" lines_diff="48">
651 <assert_contents>
652 <has_n_lines n="67"/>
653 </assert_contents>
654 </output>
644 </test> 655 </test>
645 <test> 656 <test expect_num_outputs='1'>
646 <conditional name="mode"> 657 <conditional name="mode">
647 <param name="mode_parameters" value="tumor_only"/> 658 <param name="mode_parameters" value="tumor_only"/>
648 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" /> 659 <param name="tumor" ftype="bam" value="Mutect2-in4.bam" />
649 </conditional> 660 </conditional>
650 <param name="reference_sequence" value="hg38"/> 661 <param name="reference_sequence" value="hg38"/>
652 <param name="reference_source_selector" value="cached" /> 663 <param name="reference_source_selector" value="cached" />
653 <param name="reference_sequence" value="hg38"/> 664 <param name="reference_sequence" value="hg38"/>
654 <param name="optional_parameters" value="no" /> 665 <param name="optional_parameters" value="no" />
655 <param name="advanced_parameters" value="no" /> 666 <param name="advanced_parameters" value="no" />
656 <param name="output_parameters" value="no" /> 667 <param name="output_parameters" value="no" />
657 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="2" /> 668 <output name="output_vcf" file="Mutect2-out4.vcf" lines_diff="48">
669 <assert_contents>
670 <has_n_lines n="85"/>
671 </assert_contents>
672 </output>
658 </test> 673 </test>
659 <test> 674 <test expect_num_outputs='3'>
660 <conditional name="mode"> 675 <conditional name="mode">
661 <param name="mode_parameters" value="tumor_only"/> 676 <param name="mode_parameters" value="tumor_only"/>
662 <param name="tumor" ftype="bam" value="Mutect2-in5.bam" /> 677 <param name="tumor" ftype="bam" value="Mutect2-in5.bam" />
663 </conditional> 678 </conditional>
664 <param name="reference_sequence" ftype="fasta" value="reference.fa" /> 679 <param name="reference_sequence" ftype="fasta" value="reference.fa" />
665 <param name="gzipped_output" value="false" /> 680 <param name="gzipped_output" value="false" />
666 <param name="reference_source_selector" value="history" /> 681 <param name="reference_source_selector" value="history" />
667 <param name="optional_parameters" value="no" /> 682 <param name="optional_parameters" value="no" />
668 <param name="advanced_parameters" value="no" /> 683 <param name="advanced_parameters" value="no" />
669 <param name="output_parameters" value="yes" /> 684 <param name="output_parameters" value="yes" />
670 <param name="debug_activity" value="true" />
671 <param name="debug_assembly" value="true" /> 685 <param name="debug_assembly" value="true" />
672 <param name="debug_bam" value="true" /> 686 <param name="debug_bam" value="true" />
673 <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="2" /> 687 <output name="output_vcf" file="Mutect2-out5.vcf" lines_diff="48">
688 <assert_contents>
689 <has_n_lines n="97"/>
690 </assert_contents>
691 </output>
674 <output name="assembly_region_out" file="Mutect2-out5-1.tabular" /> 692 <output name="assembly_region_out" file="Mutect2-out5-1.tabular" />
675 <output name="bam_output" file="Mutect2-out5.bam" /> 693 <output name="bam_output" file="Mutect2-out5.bam" ftype="bam" />
676 </test> 694 </test>
677 <test> 695 <test expect_num_outputs='1'>
678 <conditional name="mode"> 696 <conditional name="mode">
679 <param name="mode_parameters" value="somatic"/> 697 <param name="mode_parameters" value="somatic"/>
680 <param name="tumor" ftype="bam" value="tumor.bam" /> 698 <param name="tumor" ftype="bam" value="tumor.bam" />
681 <param name="normal" ftype="bam" value="normal.bam" /> 699 <param name="normal" ftype="bam" value="normal.bam" />
682 </conditional> 700 </conditional>
684 <param name="gzipped_output" value="false" /> 702 <param name="gzipped_output" value="false" />
685 <param name="reference_source_selector" value="history" /> 703 <param name="reference_source_selector" value="history" />
686 <param name="optional_parameters" value="no" /> 704 <param name="optional_parameters" value="no" />
687 <param name="advanced_parameters" value="no" /> 705 <param name="advanced_parameters" value="no" />
688 <param name="output_parameters" value="no" /> 706 <param name="output_parameters" value="no" />
689 <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="2" /> 707 <output name="output_vcf" file="Mutect2-out6.vcf" lines_diff="48">
708 <assert_contents>
709 <has_n_lines n="66"/>
710 </assert_contents>
711 </output>
690 </test> 712 </test>
691 </tests> 713 </tests>
692 <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short 714 <help><![CDATA[Call somatic short variants via local assembly of haplotypes. Short
693 variants include single nucleotide (SNV) and insertion and deletion 715 variants include single nucleotide (SNV) and insertion and deletion
694 (indel) variants. The caller combines the DREAM challenge-winning 716 (indel) variants. The caller combines the DREAM challenge-winning
695 somatic genotyping engine of the original MuTect (`Cibulskis et al., 717 somatic genotyping engine of the original MuTect (`Cibulskis et al.,
696 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__) 718 2013 <http://www.nature.com/nbt/journal/v31/n3/full/nbt.2514.html>`__)
697 with the assembly-based machinery of 719 with the assembly-based machinery of
698 `HaplotypeCaller <https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__. 720 `HaplotypeCaller <https://web.archive.org/web/20230530034638/https://gatk.broadinstitute.org/hc/en-us/articles/360035531412-HaplotypeCaller-in-a-nutshell>`__.
699 721
700 This tool is featured in the *Somatic Short Mutation calling Best 722 This tool is featured in the *Somatic Short Mutation calling Best
701 Practice Workflow*. See `this article <https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__ 723 Practice Workflow*. See `this article <https://web.archive.org/web/20230228153229/https://gatk.broadinstitute.org/hc/en-us/articles/360035531132>`__
702 for an overview of what traditional somatic calling entails, with usage examples. For the 724 for an overview of what traditional somatic calling entails, with usage examples. For the
703 latest pipeline scripts, see the `Mutect2 WDL scripts 725 latest pipeline scripts, see the `Mutect2 WDL scripts
704 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__. 726 directory <https://github.com/broadinstitute/gatk/tree/master/scripts/mutect2_wdl>`__.
705 Although we present the tool for somatic calling, it may apply to other 727 Although we present the tool for somatic calling, it may apply to other
706 contexts, such as mitochondrial variant calling. 728 contexts, such as mitochondrial variant calling.