Mercurial > repos > devteam > samtools_mpileup
annotate samtools_mpileup.xml @ 6:820754ab8901 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_mpileup commit 231882293cdd5214decddfe093612431793fdb6b-dirty
| author | devteam |
|---|---|
| date | Tue, 20 Oct 2015 16:24:54 -0400 |
| parents | aa0ef6f0ee89 |
| children | bfc4517aa037 |
| rev | line source |
|---|---|
|
6
820754ab8901
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_mpileup commit 231882293cdd5214decddfe093612431793fdb6b-dirty
devteam
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changeset
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1 <tool id="samtools_mpileup" name="MPileup" version="2.1"> |
| 4 | 2 <description>call variants</description> |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <expand macro="version_command" /> | |
| 9 <command> | |
| 10 <![CDATA[ | |
| 11 #if $reference_source.reference_source_selector == "history": | |
| 12 ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup | |
| 13 #else: | |
| 14 samtools mpileup | |
| 15 #end if | |
| 0 | 16 #if $reference_source.reference_source_selector != "history": |
| 4 | 17 -f "${reference_source.ref_file.fields.path}" |
| 0 | 18 #else: |
| 4 | 19 -f "${reference_source.ref_file}" |
| 0 | 20 #end if |
| 21 #for $i, $input_bam in enumerate( $reference_source.input_bams ): | |
| 4 | 22 "${input_bam.input_bam}" |
| 0 | 23 #end for |
| 24 #if str( $advanced_options.advanced_options_selector ) == "advanced": | |
| 4 | 25 #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter": |
| 26 #if $advanced_options.filter_by_flags.require_flags: | |
| 27 --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])} | |
| 28 #end if | |
| 29 #if $advanced_options.filter_by_flags.exclude_flags: | |
| 30 --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(',')])} | |
| 31 #end if | |
| 32 #end if | |
| 33 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": | |
| 34 -l "$pasted_regions" | |
| 35 #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history" | |
|
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aa0ef6f0ee89
planemo upload commit 7d9b478cd03f31705266596fe4c168e719c672b6
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36 -l "$advanced_options.limit_by_region.bed_regions" |
| 4 | 37 #end if |
| 38 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": | |
| 39 -G "$excluded_read_groups" | |
| 40 #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history" | |
|
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aa0ef6f0ee89
planemo upload commit 7d9b478cd03f31705266596fe4c168e719c672b6
devteam
parents:
4
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changeset
|
41 -G "$advanced_options.exclude_read_group.read_groups" |
| 4 | 42 #end if |
|
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aa0ef6f0ee89
planemo upload commit 7d9b478cd03f31705266596fe4c168e719c672b6
devteam
parents:
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changeset
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43 ${advanced_options.skip_anomalous_read_pairs} |
| 0 | 44 ${advanced_options.disable_probabilistic_realignment} |
| 45 -C "${advanced_options.coefficient_for_downgrading}" | |
| 46 -d "${advanced_options.max_reads_per_bam}" | |
| 47 ${advanced_options.extended_BAQ_computation} | |
| 48 -q "${advanced_options.minimum_mapping_quality}" | |
| 49 -Q "${advanced_options.minimum_base_quality}" | |
| 50 #if str( $advanced_options.region_string ): | |
| 51 -r "${advanced_options.region_string}" | |
| 52 #end if | |
| 4 | 53 |
| 0 | 54 #end if |
| 55 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation': | |
| 4 | 56 ## |
| 57 | |
| 58 ${genotype_likelihood_computation_type.output_format} | |
| 59 ${genotype_likelihood_computation_type.compressed} | |
| 60 | |
| 61 #if str( $genotype_likelihood_computation_type.output_tags ) != "None": | |
|
6
820754ab8901
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_mpileup commit 231882293cdd5214decddfe093612431793fdb6b-dirty
devteam
parents:
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diff
changeset
|
62 --output-tags "${genotype_likelihood_computation_type.output_tags}" |
| 4 | 63 #end if |
| 64 | |
| 0 | 65 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling': |
| 4 | 66 -o "${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}" |
| 67 -e "${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}" | |
| 68 -h "${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}" | |
| 0 | 69 -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}" |
| 4 | 70 -m "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" |
| 71 --open-prob "${genotype_likelihood_computation_type.perform_indel_calling.open_seq_error_probability}" | |
| 72 -F "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}" | |
| 73 ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample} | |
| 74 #if len( $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ): | |
| 75 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }" | |
| 76 #end if | |
| 77 #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling': | |
| 0 | 78 -I |
| 79 #end if | |
| 4 | 80 |
| 81 | |
| 82 #else: | |
| 83 ${genotype_likelihood_computation_type.base_position_on_reads} | |
| 84 ${genotype_likelihood_computation_type.output_mapping_quality} | |
| 0 | 85 #end if |
| 4 | 86 --output "$output_mpileup" 2> "$output_log" |
| 87 ]]> | |
| 88 </command> | |
| 89 <inputs> | |
| 90 <conditional name="reference_source"> | |
| 91 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select"> | |
| 92 <option value="cached">Use a built-in genome</option> | |
| 93 <option value="history">Use a genome from the history</option> | |
| 94 </param> | |
| 95 <when value="cached"> | |
| 96 <repeat min="1" name="input_bams" title="BAM file"> | |
| 97 <param format="bam" label="BAM file" name="input_bam" type="data"> | |
| 98 <validator type="unspecified_build" /> | |
| 99 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> | |
| 100 </param> | |
| 101 </repeat> | |
| 102 <param label="Using reference genome" name="ref_file" type="select"> | |
| 103 <options from_data_table="fasta_indexes" /> | |
| 104 </param> | |
| 105 </when> | |
| 106 <when value="history"> | |
| 107 <repeat min="1" name="input_bams" title="BAM file"> | |
| 108 <param format="bam" label="BAM file" name="input_bam" type="data"> | |
| 109 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> | |
| 110 </param> | |
| 111 </repeat> | |
| 112 <param format="fasta" label="Using reference genome" name="ref_file" type="data" /> | |
| 113 </when> | |
| 114 </conditional> | |
| 115 <conditional name="genotype_likelihood_computation_type"> | |
| 116 <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select"> | |
| 117 <option selected="True" value="perform_genotype_likelihood_computation">Perform genotype likelihood computation (--VCF, --BCF options)</option> | |
| 118 <option value="do_not_perform_genotype_likelihood_computation">Do not perform genotype likelihood computation (output pileup)</option> | |
| 0 | 119 </param> |
| 4 | 120 <when value="perform_genotype_likelihood_computation"> |
| 121 <param label="Choose the output format" name="output_format" type="select"> | |
| 122 <option value="--VCF">VCF</option> | |
| 123 <option value="--BCF">BCF</option> | |
| 124 </param> | |
| 125 <param checked="False" falsevalue="--uncompressed" label="Compress output" name="compressed" truevalue="" type="boolean" help="--incompressed; default=False"/> | |
| 126 <param name="output_tags" optional="True" type="select" multiple="True" display="checkboxes" label="Optional tags to output" help="--output-tags"> | |
| 127 <option value="DP">DP (Number of high-quality bases)</option> | |
| 128 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option> | |
| 129 <option value="DV">DV (Number of high-quality non-reference bases)</option> | |
| 130 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option> | |
| 131 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option> | |
| 132 <option value="SP">SP (Phred-scaled strand bias P-value)</option> | |
| 133 </param> | |
| 134 <conditional name="perform_indel_calling"> | |
| 135 <param label="Perform INDEL calling" name="perform_indel_calling_selector" type="select"> | |
| 136 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option> | |
| 137 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option> | |
| 138 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option> | |
| 139 </param> | |
| 140 <when value="perform_indel_calling_def" /> | |
| 141 <when value="perform_indel_calling"> | |
| 142 <param label="Phred-scaled gap open sequencing error probability" name="gap_open_sequencing_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> | |
| 143 <param label="Phred-scaled gap extension sequencing error probability" name="gap_extension_sequencing_error_probability" type="integer" value="20" help="--ext-prob; Reducing this value leads to longer indels. default=20"/> | |
| 144 <param label="Coefficient for modeling homopolymer errors." name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" help="--tandem-qual; default=100"/> | |
| 145 <param label="Skip INDEL calling if the average per-sample depth is above" name="skip_indel_calling_above_sample_depth" type="integer" value="250" help="--max-idepth; default=250"/> | |
| 146 <param label="Minimum gapped reads for indel candidates" name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" help="--min-ireads; default=1"/> | |
| 147 <param label="Phred-scaled gap open sequencing error probability" name="open_seq_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> | |
| 148 <param label="Minimum fraction of gapped reads" name="minimum_gapped_read_fraction" type="float" value="0.002" help="--gap-frac; default=0.002"/> | |
| 149 <param checked="False" falsevalue="" label="Apply --min-ireads and --gap-frac values on a per-sample basis" name="gapped_read_per_sample" truevalue="-p" type="boolean" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/> | |
| 150 <repeat name="platform_list_repeat" title="Platform for INDEL candidates"> | |
| 151 <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/> | |
| 152 </repeat> | |
| 153 </when> | |
| 154 <when value="do_not_perform_indel_calling" /> | |
| 155 </conditional> | |
| 156 | |
| 157 </when> | |
| 158 <when value="do_not_perform_genotype_likelihood_computation"> | |
| 159 <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/> | |
| 160 <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/> | |
| 0 | 161 </when> |
| 4 | 162 </conditional> |
| 163 <conditional name="advanced_options"> | |
| 164 <param label="Set advanced options" name="advanced_options_selector" type="select"> | |
| 165 <option selected="True" value="basic">Basic</option> | |
| 166 <option value="advanced">Advanced</option> | |
| 167 </param> | |
| 168 <when value="advanced"> | |
| 169 <conditional name="filter_by_flags"> | |
| 170 <param label="Set filter by flags" name="filter_flags" type="select"> | |
| 171 <option selected="True" value="nofilter">Do not filter</option> | |
| 172 <option value="filter">Filter by flags to exclude or require</option> | |
| 173 </param> | |
| 174 <when value="filter"> | |
| 175 <param display="checkboxes" label="Require" multiple="True" name="require_flags" type="select" help="--incl-flags"> | |
| 176 <option value="1">Read is paired</option> | |
| 177 <option value="2">Read is mapped in a proper pair</option> | |
| 178 <option value="4">The read is unmapped</option> | |
| 179 <option value="8">The mate is unmapped</option> | |
| 180 <option value="16">Read strand</option> | |
| 181 <option value="32">Mate strand</option> | |
| 182 <option value="64">Read is the first in a pair</option> | |
| 183 <option value="128">Read is the second in a pair</option> | |
| 184 <option value="256">The alignment or this read is not primary</option> | |
| 185 <option value="512">The read fails platform/vendor quality checks</option> | |
| 186 <option value="1024">The read is a PCR or optical duplicate</option> | |
| 187 </param> | |
| 188 <param display="checkboxes" label="Exclude" multiple="True" name="exclude_flags" type="select" help="--excl-flags"> | |
| 189 <option value="1">Read is paired</option> | |
| 190 <option value="2">Read is mapped in a proper pair</option> | |
| 191 <option value="4">The read is unmapped</option> | |
| 192 <option value="8">The mate is unmapped</option> | |
| 193 <option value="16">Read strand</option> | |
| 194 <option value="32">Mate strand</option> | |
| 195 <option value="64">Read is the first in a pair</option> | |
| 196 <option value="128">Read is the second in a pair</option> | |
| 197 <option value="256">The alignment or this read is not primary</option> | |
| 198 <option value="512">The read fails platform/vendor quality checks</option> | |
| 199 <option value="1024">The read is a PCR or optical duplicate</option> | |
| 200 </param> | |
| 201 </when> | |
| 202 <when value="nofilter" /> | |
| 203 </conditional> | |
| 204 <conditional name="limit_by_region"> | |
| 205 <param label="Select regions to call" name="limit_by_regions" type="select"> | |
| 206 <option selected="True" value="no_limit">Do not limit</option> | |
| 207 <option value="history">From an uploaded BED file (--positions)</option> | |
| 208 <option value="paste">Paste a list of regions or BED (--region)</option> | |
| 209 </param> | |
| 210 <when value="history"> | |
| 211 <param format="bed" label="BED file" name="bed_regions" type="data" help="--positions"> | |
| 212 <validator type="dataset_ok_validator" /> | |
| 213 </param> | |
| 214 </when> | |
| 215 <when value="paste"> | |
| 216 <param area="true" help="Paste a list of regions in BED format or as a list of chromosomes and positions" label="Regions" name="region_paste" size="10x35" type="text"/> | |
| 217 </when> | |
| 218 <when value="no_limit" /> | |
| 219 </conditional> | |
| 220 <conditional name="exclude_read_group"> | |
| 221 <param label="Select read groups to exclude" name="exclude_read_groups" type="select" help="--exclude-RG"> | |
| 222 <option selected="True" value="no_limit">Do not exclude</option> | |
| 223 <option value="history">From an uploaded text file</option> | |
| 224 <option value="paste">Paste a list of read groups</option> | |
| 225 </param> | |
| 226 <when value="history"> | |
| 227 <param format="txt" label="Text file" name="read_groups" type="data"> | |
| 228 <validator type="dataset_ok_validator" /> | |
| 229 </param> | |
| 230 </when> | |
| 231 <when value="paste"> | |
| 232 <param area="true" help="Paste a list of read groups" label="Read groups" name="group_paste" size="10x35" type="text" /> | |
| 233 </when> | |
| 234 <when value="no_limit" /> | |
| 235 </conditional> | |
| 236 <param checked="False" falsevalue="" label="Disable read-pair overlap detection" name="ignore_overlaps" truevalue="-x" type="boolean" help="--ignore-overlaps"/> | |
| 237 <param checked="False" falsevalue="" label="Do not skip anomalous read pairs in variant calling" name="skip_anomalous_read_pairs" truevalue="-A" type="boolean" help="--count-orphans"/> | |
| 238 <param checked="False" falsevalue="" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" name="disable_probabilistic_realignment" truevalue="-B" type="boolean" help="--no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments"/> | |
| 239 <param label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" name="coefficient_for_downgrading" type="integer" value="0" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/> | |
| 240 <param label="Max reads per BAM" max="1024" min="1" name="max_reads_per_bam" type="integer" value="250" help="--max-depth; default=250"/> | |
| 241 <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/> | |
| 242 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/> | |
| 243 <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/> | |
|
5
aa0ef6f0ee89
planemo upload commit 7d9b478cd03f31705266596fe4c168e719c672b6
devteam
parents:
4
diff
changeset
|
244 <param label="Only generate pileup in region" name="region_string" type="text" value="" help="--region; If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" /> |
| 4 | 245 </when> |
| 246 <when value="basic" /> | |
| 247 </conditional> | |
| 248 </inputs> | |
| 249 <outputs> | |
| 250 <data format="pileup" label="${tool.name} on ${on_string}" name="output_mpileup"> | |
| 251 <change_format> | |
| 252 <when format="bcf" input="genotype_likelihood_computation_type.output_format" value="--BCF" /> | |
| 253 <when format="vcf" input="genotype_likelihood_computation_type.output_format" value="--VCF" /> | |
| 254 </change_format> | |
| 255 </data> | |
| 256 <data format="txt" label="${tool.name} on ${on_string} (log)" name="output_log" /> | |
| 257 </outputs> | |
| 258 <tests> | |
| 259 <test> | |
| 260 <param name="reference_source_selector" value="history" /> | |
| 261 <param ftype="fasta" name="ref_file" value="phiX.fasta" /> | |
| 262 <param ftype="bam" name="input_bam" value="samtools_mpileup_in_1.bam" /> | |
| 263 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" /> | |
| 264 <param name="advanced_options_selector" value="basic" /> | |
| 265 <param name="base_position_on_reads" value="true" /> | |
| 266 <param name="output_mapping_quality" value="true" /> | |
| 267 <output file="samtools_mpileup_out_1.pileup" name="output_mpileup" /> | |
| 268 <output file="samtools_mpileup_out_1.log" name="output_log" /> | |
| 269 </test> | |
| 270 <test> | |
| 271 <param name="reference_source_selector" value="history" /> | |
| 272 <param ftype="fasta" name="ref_file" value="phiX.fasta" /> | |
| 273 <param ftype="bam" name="input_bam" value="phiX.bam" /> | |
| 274 <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" /> | |
| 275 <param name="gap_extension_sequencing_error_probability" value="20" /> | |
| 276 <param name="coefficient_for_modeling_homopolymer_errors" value="100" /> | |
| 277 <param name="perform_indel_calling_selector" value="perform_indel_calling" /> | |
| 278 <param name="skip_indel_calling_above_sample_depth" value="250" /> | |
| 279 <param name="gap_open_sequencing_error_probability" value="40" /> | |
| 280 <param name="platform_list_repeat" value="0" /> | |
| 281 <param name="advanced_options_selector" value="basic" /> | |
| 282 <param name="genotype_likelihood_computation_type|output_format" value="VCF" /> | |
| 283 <output file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" name="output_mpileup" /> | |
| 284 <output file="samtools_mpileup_out_2.log" name="output_log" /> | |
| 285 </test> | |
| 286 </tests> | |
| 287 <help> | |
| 288 <![CDATA[ | |
| 0 | 289 **What it does** |
| 290 | |
| 4 | 291 Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. |
| 0 | 292 |
| 293 ------ | |
| 294 | |
| 4 | 295 **Input options**:: |
| 296 | |
| 297 -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding | |
| 298 -A, --count-orphans do not discard anomalous read pairs | |
| 299 -b, --bam-list FILE list of input BAM filenames, one per line | |
| 300 -B, --no-BAQ disable BAQ (per-Base Alignment Quality) | |
| 301 -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0] | |
| 302 -d, --max-depth INT max per-BAM depth; avoids excessive memory usage [250] | |
| 303 -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs | |
| 304 -f, --fasta-ref FILE faidx indexed reference sequence file | |
| 305 -G, --exclude-RG FILE exclude read groups listed in FILE | |
| 306 -l, --positions FILE skip unlisted positions (chr pos) or regions (BED) | |
| 307 -q, --min-MQ INT skip alignments with mapQ smaller than INT [0] | |
| 308 -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13] | |
| 309 -r, --region REG region in which pileup is generated | |
| 310 -R, --ignore-RG ignore RG tags (one BAM = one sample) | |
| 311 --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset [] | |
| 312 --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set | |
| 313 [UNMAP,SECONDARY,QCFAIL,DUP] | |
| 314 -x, --ignore-overlaps disable read-pair overlap detection | |
| 315 | |
| 316 **Output options**:: | |
| 317 | |
| 318 -o, --output FILE write output to FILE [standard output] | |
| 319 -g, --BCF generate genotype likelihoods in BCF format | |
| 320 -v, --VCF generate genotype likelihoods in VCF format | |
| 321 | |
| 322 **Output options for mpileup format** (without -g/-v):: | |
| 323 | |
| 324 -O, --output-BP output base positions on reads | |
| 325 -s, --output-MQ output mapping quality | |
| 326 | |
| 327 **Output options for genotype likelihoods** (when -g/-v is used):: | |
| 328 | |
| 329 -t, --output-tags LIST optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP [] | |
| 330 -u, --uncompressed generate uncompressed VCF/BCF output | |
| 331 | |
| 332 **SNP/INDEL genotype likelihoods options** (effective with -g/-v):: | |
| 0 | 333 |
| 4 | 334 -e, --ext-prob INT Phred-scaled gap extension seq error probability [20] |
| 335 -F, --gap-frac FLOAT minimum fraction of gapped reads [0.002] | |
| 336 -h, --tandem-qual INT coefficient for homopolymer errors [100] | |
| 337 -I, --skip-indels do not perform indel calling | |
| 338 -L, --max-idepth INT maximum per-sample depth for INDEL calling [250] | |
| 339 -m, --min-ireads INT minimum number gapped reads for indel candidates [1] | |
| 340 -o, --open-prob INT Phred-scaled gap open seq error probability [40] | |
| 341 -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity | |
| 342 -P, --platforms STR comma separated list of platforms for indels [all] | |
| 0 | 343 |
| 4 | 344 **Notes**: Assuming diploid individuals. |
| 345 ]]> | |
| 346 </help> | |
| 347 <configfiles> | |
| 348 <configfile name="excluded_read_groups"> | |
| 349 <![CDATA[ | |
| 350 #set pasted_data = '' | |
| 351 #if str( $advanced_options.advanced_options_selector ) == "advanced": | |
| 352 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": | |
| 353 #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() ) | |
| 354 #end if | |
| 355 #end if | |
| 356 ${pasted_data} | |
| 357 ]]> | |
| 358 </configfile> | |
| 359 <configfile name="pasted_regions"> | |
| 360 <![CDATA[ | |
| 361 #set pasted_data = '' | |
| 362 #if str( $advanced_options.advanced_options_selector ) == "advanced": | |
| 363 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": | |
| 364 #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() ) | |
| 365 #end if | |
| 366 #end if | |
| 367 ${pasted_data} | |
| 368 ]]> | |
| 369 </configfile> | |
| 370 </configfiles> | |
| 371 <expand macro="citations" /> | |
| 0 | 372 </tool> |