Mercurial > repos > iuc > gatk2
annotate unified_genotyper.xml @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 05:38:15 -0400 |
| parents | f244b8209eb8 |
| children |
| rev | line source |
|---|---|
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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1 <tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.2"> |
| 0 | 2 <description>SNP and indel caller</description> |
| 3 <macros> | |
| 4 <import>gatk2_macros.xml</import> | |
| 5 </macros> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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6 <expand macro="requirements" /> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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7 <expand macro="version_command" /> |
| 0 | 8 <command interpreter="python"> |
| 9 gatk2_wrapper.py | |
| 10 --stdout "${output_log}" | |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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11 @BAM_INPUTS@ |
| 0 | 12 -p ' |
| 13 @JAR_PATH@ | |
| 14 -T "UnifiedGenotyper" | |
| 15 @THREADS@ | |
| 16 --out "${output_vcf}" | |
| 17 --metrics_file "${output_metrics}" | |
| 18 \$GATK2_SITE_OPTIONS | |
| 19 | |
| 20 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975 | |
| 3 | 21 --num_cpu_threads_per_data_thread 1 |
| 0 | 22 |
| 23 #if $reference_source.reference_source_selector != "history": | |
| 24 -R "${reference_source.ref_file.fields.path}" | |
| 25 #end if | |
| 26 --genotype_likelihoods_model "${genotype_likelihoods_model}" | |
| 27 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}" | |
| 28 --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" | |
| 29 ' | |
| 2 | 30 @DBSNP_OPTIONS@ |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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changeset
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31 $allow_n_cigar_reads |
| 0 | 32 #include source=$standard_gatk_options# |
| 33 ##start analysis specific options | |
| 34 #if $analysis_param_type.analysis_param_type_selector == "advanced": | |
| 35 -p ' | |
| 36 --heterozygosity "${analysis_param_type.heterozygosity}" | |
| 37 --pcr_error_rate "${analysis_param_type.pcr_error_rate}" | |
| 38 --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}" | |
| 39 #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES': | |
| 40 --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}" | |
| 41 #end if | |
| 42 --output_mode "${analysis_param_type.output_mode}" | |
| 43 ${analysis_param_type.compute_SLOD} | |
| 44 --min_base_quality_score "${analysis_param_type.min_base_quality_score}" | |
| 45 --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}" | |
| 46 --max_alternate_alleles "${analysis_param_type.max_alternate_alleles}" | |
| 47 --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}" | |
| 48 --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}" | |
| 49 --indelGapContinuationPenalty "${analysis_param_type.indelGapContinuationPenalty}" | |
| 50 --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}" | |
| 51 --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}" | |
| 52 ${analysis_param_type.doContextDependentGapPenalties} | |
| 53 #if str( $analysis_param_type.annotation ) != "None": | |
| 54 #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','): | |
| 55 --annotation "${annotation}" | |
| 56 #end for | |
| 57 #end if | |
| 58 #for $additional_annotation in $analysis_param_type.additional_annotations: | |
| 59 --annotation "${additional_annotation.additional_annotation_name}" | |
| 60 #end for | |
| 61 #if str( $analysis_param_type.group ) != "None": | |
| 62 #for $group in str( $analysis_param_type.group ).split( ','): | |
| 63 --group "${group}" | |
| 64 #end for | |
| 65 #end if | |
| 66 #if str( $analysis_param_type.exclude_annotations ) != "None": | |
| 67 #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','): | |
| 68 --excludeAnnotation "${annotation}" | |
| 69 #end for | |
| 70 #end if | |
| 71 #if str( $analysis_param_type.sample_ploidy ) != '': | |
| 72 --sample_ploidy "$analysis_param_type.sample_ploidy" | |
| 73 #end if | |
| 74 ' | |
| 75 ## #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff': | |
| 76 ## -p '--annotation "SnpEff"' | |
| 77 ## -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}" | |
| 78 ## #else: | |
| 79 ## -p '--excludeAnnotation "SnpEff"' | |
| 80 ## #end if | |
| 81 #end if | |
| 82 </command> | |
| 83 <inputs> | |
| 84 <conditional name="reference_source"> | |
| 85 <expand macro="reference_source_selector_param" /> | |
| 86 <when value="cached"> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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changeset
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87 <expand macro="input_bams_cached" /> |
| 0 | 88 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> |
| 89 <options from_data_table="gatk2_picard_indexes"> | |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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90 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> |
| 0 | 91 </options> |
| 92 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
| 93 </param> | |
| 94 </when> | |
| 95 <when value="history"> <!-- FIX ME!!!! --> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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96 <expand macro="input_bams_history" /> |
| 0 | 97 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> |
| 98 </when> | |
| 99 </conditional> | |
| 2 | 100 <expand macro="dbsnp_param" /> |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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101 |
| 0 | 102 <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &lt;genotype_likelihoods_model&gt;"> |
| 103 <option value="BOTH" selected="True">BOTH</option> | |
| 104 <option value="SNP">SNP</option> | |
| 105 <option value="INDEL">INDEL</option> | |
| 106 </param> | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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107 |
| 0 | 108 <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &lt;standard_min_confidence_threshold_for_calling&gt;" /> |
| 109 <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &lt;standard_min_confidence_threshold_for_emitting&gt;" /> | |
| 110 | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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diff
changeset
|
111 <expand macro="allow_n_cigar_reads" /> |
| 0 | 112 <expand macro="gatk_param_type_conditional" /> |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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diff
changeset
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113 |
| 0 | 114 <expand macro="analysis_type_conditional"> |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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changeset
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115 <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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116 help="-hets,--heterozygosity &lt;heterozygosity&gt;" /> |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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|
117 <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
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118 help="-pcr_error,--pcr_error_rate &lt;pcr_error_rate&gt;" /> |
| 0 | 119 <conditional name="genotyping_mode_type"> |
| 120 <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &lt;genotyping_mode&gt;"> | |
| 121 <option value="DISCOVERY" selected="True">DISCOVERY</option> | |
| 122 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> | |
| 123 </param> | |
| 124 <when value="DISCOVERY"> | |
| 125 <!-- Do nothing here --> | |
| 126 </when> | |
| 127 <when value="GENOTYPE_GIVEN_ALLELES"> | |
| 128 <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &lt;alleles&gt;" /> | |
| 129 </when> | |
| 130 </conditional> | |
| 131 <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?" help="-out_mode,--output_mode &lt;output_mode&gt;"> | |
| 132 <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option> | |
| 133 <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option> | |
| 134 <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option> | |
| 135 </param> | |
| 136 <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" /> | |
| 137 <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &lt;min_base_quality_score&gt;" /> | |
| 138 <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to < 0 or > 1 (-deletions,--max_deletion_fraction &lt;max_deletion_fraction&gt;)" /> | |
| 139 <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &lt;max_alternate_alleles&gt;" /> | |
| 140 <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &lt;min_indel_count_for_genotyping&gt;" /> | |
| 141 <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &lt;indel_heterozygosity&gt;)"/> | |
| 2 | 142 <param name="indelGapContinuationPenalty" type="integer" value="10" label="Indel gap continuation penalty" help="As Phred-scaled probability, i.e. 30 => 10^-30/10 (--indelGapContinuationPenalty)"> |
| 143 <validator type="in_range" message="value between 0 and 255" min="0" max="255" /> | |
| 0 | 144 </param> |
| 2 | 145 <param name="indelGapOpenPenalty" type="integer" value="45" label="Indel gap open penalty" help="As Phred-scaled probability, i.e. 30 => 10^-30/10 (--indelGapOpenPenalty)"> |
| 146 <validator type="in_range" message="value between 0 and 255" min="0" max="255" /> | |
| 0 | 147 </param> |
| 148 <!-- indelHaplotypeSize - Gone in GATK 2.4? --> | |
| 149 <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" /> | |
| 150 <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" /> | |
| 151 <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &lt;annotation&gt;"> | |
| 152 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> | |
| 153 <options from_data_table="gatk2_annotations"> | |
| 154 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | |
| 155 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> | |
| 156 </options> | |
| 157 </param> | |
| 158 <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &lt;annotation&gt;"> | |
| 159 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> | |
| 160 </repeat> | |
| 161 <!-- | |
| 162 <conditional name="snpEff_rod_bind_type"> | |
| 163 <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file"> | |
| 164 <option value="set_snpEff">Set snpEff</option> | |
| 165 <option value="exclude_snpEff" selected="True">Don't set snpEff</option> | |
| 166 </param> | |
| 167 <when value="exclude_snpEff"> | |
| 168 </when> | |
| 169 <when value="set_snpEff"> | |
| 170 <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" /> | |
| 171 <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/> | |
| 172 </when> | |
| 173 </conditional> | |
| 174 --> | |
| 175 <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &lt;group&gt;"> | |
| 176 <option value="RodRequiringAnnotation">RodRequiringAnnotation</option> | |
| 177 <option value="Standard">Standard</option> | |
| 178 <option value="Experimental">Experimental</option> | |
| 179 <option value="WorkInProgress">WorkInProgress</option> | |
| 180 <option value="RankSumTest">RankSumTest</option> | |
| 181 <!-- <option value="none">none</option> --> | |
| 182 </param> | |
| 183 <!-- <param name="family_string" type="text" value="" label="Family String"/> --> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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184 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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185 help="-XA,--excludeAnnotation &lt;excludeAnnotation&gt;" > |
| 0 | 186 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> |
| 187 <options from_data_table="gatk2_annotations"> | |
| 188 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> | |
| 189 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> | |
| 190 </options> | |
| 191 </param> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
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192 <param name="sample_ploidy" type="integer" value="2" |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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diff
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|
193 label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,--sample_ploidy" /> |
| 0 | 194 </expand> |
| 195 </inputs> | |
| 196 <outputs> | |
| 197 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> | |
| 198 <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /> | |
| 199 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> | |
| 200 </outputs> | |
| 201 <trackster_conf/> | |
| 202 <tests> | |
| 203 <test> | |
| 204 <param name="reference_source_selector" value="history" /> | |
| 205 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> | |
| 206 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" /> | |
| 2 | 207 <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /> |
| 208 <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> | |
| 209 <param name="dbsnp_rod_name" value="dbsnp" /> | |
| 0 | 210 <param name="standard_min_confidence_threshold_for_calling" value="0" /> |
| 211 <param name="standard_min_confidence_threshold_for_emitting" value="4" /> | |
| 212 <param name="gatk_param_type_selector" value="basic" /> | |
| 213 <param name="analysis_param_type_selector" value="advanced" /> | |
| 214 <param name="genotype_likelihoods_model" value="BOTH" /> | |
| 215 <param name="heterozygosity" value="0.001" /> | |
| 216 <param name="pcr_error_rate" value="0.0001" /> | |
| 217 <param name="genotyping_mode" value="DISCOVERY" /> | |
| 218 <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" /> | |
| 219 <param name="compute_SLOD" /> | |
| 220 <param name="min_base_quality_score" value="17" /> | |
| 221 <param name="max_deletion_fraction" value="-1" /> | |
| 222 <param name="min_indel_count_for_genotyping" value="2" /> | |
| 223 <param name="indel_heterozygosity" value="0.000125" /> | |
| 224 <param name="indelGapContinuationPenalty" value="10" /> | |
| 225 <param name="indelGapOpenPenalty" value="3" /> | |
| 226 <param name="indelHaplotypeSize" value="80" /> | |
| 227 <param name="doContextDependentGapPenalties" /> | |
| 228 <!-- <param name="annotation" value="" /> | |
| 229 <param name="group" value="" /> --> | |
|
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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diff
changeset
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230 <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
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diff
changeset
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231 <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> |
| 0 | 232 <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" /> |
| 233 </test> | |
| 234 </tests> | |
| 235 <help> | |
| 236 **What it does** | |
| 237 | |
| 238 A variant caller which unifies the approaches of several disparate callers. Works for single-sample and multi-sample data. The user can choose from several different incorporated calculation models. | |
| 239 | |
| 240 For more information on the GATK Unified Genotyper, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html>`_. | |
| 241 | |
| 242 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | |
| 243 | |
| 244 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | |
| 245 | |
| 246 ------ | |
| 247 | |
| 248 **Inputs** | |
| 249 | |
| 250 GenomeAnalysisTK: UnifiedGenotyper accepts an aligned BAM input file. | |
| 251 | |
| 252 | |
| 253 **Outputs** | |
| 254 | |
| 255 The output is in VCF format. | |
| 256 | |
| 257 | |
| 258 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats. | |
| 259 | |
| 260 ------- | |
| 261 | |
| 262 **Settings**:: | |
| 263 | |
| 264 genotype_likelihoods_model Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only (SNP|INDEL|BOTH) | |
| 265 heterozygosity Heterozygosity value used to compute prior likelihoods for any locus | |
| 266 pcr_error_rate The PCR error rate to be used for computing fragment-based likelihoods | |
| 267 genotyping_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES) | |
| 268 output_mode Should we output confident genotypes (i.e. including ref calls) or just the variants? (EMIT_VARIANTS_ONLY|EMIT_ALL_CONFIDENT_SITES|EMIT_ALL_SITES) | |
| 269 standard_min_confidence_threshold_for_calling The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called | |
| 270 standard_min_confidence_threshold_for_emitting The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold) | |
| 271 noSLOD If provided, we will not calculate the SLOD | |
| 272 min_base_quality_score Minimum base quality required to consider a base for calling | |
| 273 max_deletion_fraction Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05] | |
| 274 min_indel_count_for_genotyping Minimum number of consensus indels required to trigger genotyping run | |
| 275 indel_heterozygosity Heterozygosity for indel calling | |
| 276 indelGapContinuationPenalty Indel gap continuation penalty | |
| 277 indelGapOpenPenalty Indel gap open penalty | |
| 278 indelHaplotypeSize Indel haplotype size | |
| 279 doContextDependentGapPenalties Vary gap penalties by context | |
| 280 indel_recal_file Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE | |
| 281 indelDebug Output indel debug info | |
| 282 out File to which variants should be written | |
| 283 annotation One or more specific annotations to apply to variant calls | |
| 284 group One or more classes/groups of annotations to apply to variant calls | |
| 285 | |
| 286 @CITATION_SECTION@ | |
| 287 </help> | |
| 4 | 288 <expand macro="citations" /> |
| 0 | 289 </tool> |