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comparison variant_select.xml @ 15:01ff8dd37d4d draft default tip

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author lz_hust
date Sat, 01 Jun 2019 07:20:41 -0400
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14:68426930d59c 15:01ff8dd37d4d
1 <tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.2">
2 <description>from VCF files</description>
3 <macros>
4 <import>gatk2_macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command interpreter="python">
9 #from binascii import hexlify
10
11 gatk2_wrapper.py
12 --stdout "${output_log}"
13 -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
14 -p '
15 @JAR_PATH@
16 -T "SelectVariants"
17 \$GATK2_SITE_OPTIONS
18
19 @THREADS@
20 -o "${output_vcf}"
21
22 #if $reference_source.reference_source_selector != "history":
23 -R "${reference_source.ref_file.fields.path}"
24 #end if
25 '
26 -p '
27 #if $input_concordance:
28 --concordance "${input_concordance}"
29 #end if
30 #if $input_discordance:
31 --discordance "${input_discordance}"
32 #end if
33
34 #for $exclude_sample_name in $exclude_sample_name_repeat:
35 --exclude_sample_name "${exclude_sample_name.exclude_sample_name}"
36 #end for
37
38 ${exclude_filtered}
39
40 #for $sample_name in $sample_name_repeat:
41 --sample_name "${sample_name.sample_name}"
42 #end for
43 '
44
45 #for $select_expressions in $select_expressions_repeat:
46 #set $select_expression = "--select_expressions '%s'" % ( str( $select_expressions.select_expressions ) )
47 -o '${ hexlify( $select_expression ) }'
48 #end for
49
50 ##start tool specific options
51 #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced':
52 -p '
53 #for $esf in $analysis_param_type.exclude_sample_file:
54 --exclude_sample_file "${esf}"
55 #end for
56
57 #for $sf in $analysis_param_type.sample_file:
58 --sample_file "${sf}"
59 #end for
60
61 #if $analysis_param_type.input_keep_ids:
62 --keepIDs "${analysis_param_type.input_keep_ids}"
63 #end if
64
65 ${analysis_param_type.keep_original_AC}
66
67 ${analysis_param_type.mendelian_violation}
68
69 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
70
71 --remove_fraction_genotypes "${analysis_param_type.remove_fraction_genotypes}"
72
73 --restrictAllelesTo "${analysis_param_type.restrict_alleles_to}"
74
75 #if str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_fraction':
76 --select_random_fraction "${analysis_param_type.select_random_type.select_random_fraction}"
77 #elif str( $analysis_param_type.select_random_type.select_random_type_selector ) == 'select_random_number':
78 --select_random_number "${analysis_param_type.select_random_type.select_random_number}"
79 #end if
80
81 #if $analysis_param_type.select_type_to_include:
82 #for $type_to_include in str( $analysis_param_type.select_type_to_include ).split( ',' ):
83 --selectTypeToInclude "${type_to_include}"
84 #end for
85 #end if
86
87 ${analysis_param_type.exclude_non_variants}
88 '
89
90 #for $sample_expressions in $analysis_param_type.sample_expressions_repeat:
91 #set $sample_expression = "--sample_expressions '%s'" % ( str( $sample_expressions.sample_expressions ) )
92 -o '${ hexlify( $sample_expression ) }'
93 #end for
94
95 #end if
96 ##end tool specific options
97
98 #include source=$standard_gatk_options#
99 </command>
100 <inputs>
101 <conditional name="reference_source">
102 <expand macro="reference_source_selector_param" />
103 <when value="cached">
104 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
105 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
106 <options from_data_table="gatk2_picard_indexes">
107 <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/>
108 </options>
109 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
110 </param>
111 </when>
112 <when value="history"> <!-- FIX ME!!!! -->
113 <param name="input_variant" type="data" format="vcf" label="Variant file to select" help="-V,--variant &amp;lt;variant&amp;gt;" />
114 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
115 </when>
116 </conditional>
117
118 <repeat name="select_expressions_repeat" title="Criteria to use when selecting the data" help="-select,--select_expressions &amp;lt;select_expressions&amp;gt;">
119 <param name="select_expressions" type="text" label="JEXL expression">
120 <sanitizer>
121 <valid initial="string.printable">
122 <remove value="&apos;"/>
123 </valid>
124 <mapping initial="none"/>
125 </sanitizer>
126 </param>
127 </repeat>
128
129 <param name="input_concordance" type="data" format="vcf" label="Output variants that were also called in this comparison track" optional="True" help="-conc,--concordance &amp;lt;concordance&amp;gt;"/>
130 <param name="input_discordance" type="data" format="vcf" label="Output variants that were not called in this comparison track" optional="True" help="-disc,--discordance &amp;lt;discordance&amp;gt;"/>
131
132 <repeat name="sample_name_repeat" title="Include Samples by name" help="-sn,--sample_name &amp;lt;sample_name&amp;gt;">
133 <param name="sample_name" type="text" label="Include genotypes from this sample"/>
134 </repeat>
135
136 <repeat name="exclude_sample_name_repeat" title="Exclude Samples by name" help="-xl_sn,--exclude_sample_name &amp;lt;exclude_sample_name&amp;gt;">
137 <param name="exclude_sample_name" type="text" label="Exclude genotypes from this sample"/>
138 </repeat>
139
140 <param name="exclude_filtered" type="boolean" truevalue="--excludeFiltered" falsevalue="" label="Don't include filtered loci in the analysis" help="-ef,--excludeFiltered" />
141
142 <expand macro="gatk_param_type_conditional" />
143
144 <expand macro="analysis_type_conditional">
145
146 <param name="exclude_sample_file" type="data" format="txt" multiple="True" label="Exclude Samples by file" help="File containing a list of samples (one per line) to exclude (-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;)"/>
147
148 <param name="sample_file" type="data" format="txt" multiple="True" label="Samples by file" help="File containing a list of samples (one per line) to include (-sf,--sample_file &amp;lt;sample_file&amp;gt;)"/>
149
150 <param name="input_keep_ids" type="data" format="txt" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
151
152 <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" />
153
154 <param name="mendelian_violation" type="boolean" truevalue="--mendelianViolation" falsevalue="" label="output mendelian violation sites only" help="-mv,--mendelianViolation" />
155
156 <param name="mendelian_violation_qual_threshold" type="float" label="Minimum genotype QUAL score for each trio member required to accept a site as a mendelian violation" value="0" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;" />
157
158 <param name="remove_fraction_genotypes" type="float" label="Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall" value="0" min="0" max="1" help="-fractionGenotypes,--remove_fraction_genotypes &amp;lt;remove_fraction_genotypes&amp;gt;" />
159
160 <param name="restrict_alleles_to" type="select" label="Select only variants of a particular allelicity" help="-restrictAllelesTo,--restrictAllelesTo &amp;lt;restrictAllelesTo&amp;gt;">
161 <option value="ALL" selected="True">ALL</option>
162 <option value="MULTIALLELIC">MULTIALLELIC</option>
163 <option value="BIALLELIC">BIALLELIC</option>
164 </param>
165
166 <repeat name="sample_expressions_repeat" title="Regular expression to select many samples from the ROD tracks provided" help="-se,--sample_expressions &amp;lt;sample_expressions&amp;gt;">
167 <param name="sample_expressions" type="text" label="Regular expression">
168 <sanitizer>
169 <valid initial="string.printable">
170 <remove value="&apos;"/>
171 </valid>
172 <mapping initial="none"/>
173 </sanitizer>
174 </param>
175 </repeat>
176
177 <conditional name="select_random_type">
178 <param name="select_random_type_selector" type="select" label="Select a random subset of variants">
179 <option value="select_all" selected="True">Use all variants</option>
180 <option value="select_random_fraction">Select random fraction</option>
181 <option value="select_random_number">Select random number</option>
182 </param>
183 <when value="select_all">
184 <!-- Do nothing here -->
185 </when>
186 <when value="select_random_fraction">
187 <param name="select_random_fraction" type="float" value="0" label="Fraction" min="0" max="1" help="-fraction,--select_random_fraction &amp;lt;select_random_fraction&amp;gt;"/>
188 </when>
189 <when value="select_random_number">
190 <param name="select_random_number" type="integer" value="0" label="Count" help="-number,--select_random_number &amp;lt;select_random_number&amp;gt;" />
191 </when>
192 </conditional>
193
194 <param name="exclude_non_variants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the subsetting procedure" help="-env,--excludeNonVariants" />
195
196 <param name="select_type_to_include" type="select" label="Select only a certain type of variants from the input file" multiple="True" display="checkboxes" help="-selectType,--selectTypeToInclude &amp;lt;selectTypeToInclude&amp;gt;">
197 <option value="INDEL">INDEL</option>
198 <option value="SNP">SNP</option>
199 <option value="MIXED">MIXED</option>
200 <option value="MNP">MNP</option>
201 <option value="SYMBOLIC">SYMBOLIC</option>
202 <option value="NO_VARIATION">NO_VARIATION</option>
203 </param>
204 </expand>
205
206 </inputs>
207 <outputs>
208 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (Variant File)" />
209 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
210 </outputs>
211 <tests>
212 <test>
213 <param name="reference_source_selector" value="history" />
214 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
215 <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
216 <param name="select_expressions_repeat" value="0" />
217 <param name="input_concordance" />
218 <param name="input_discordance" />
219 <param name="exclude_sample_name_repeat" value="0" />
220 <param name="exclude_filtered" />
221 <param name="sample_name_repeat" value="0" />
222 <param name="gatk_param_type_selector" value="basic" />
223 <param name="analysis_param_type_selector" value="basic" />
224 <output name="output_vcf" file="gatk/gatk_variant_select/gatk_variant_select_out_1.vcf" lines_diff="4" />
225 <output name="output_log" file="gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains" compare="contains" />
226 </test>
227 </tests>
228 <help>
229 **What it does**
230
231 Often, a VCF containing many samples and/or variants will need to be subset in order to facilitate certain analyses (e.g. comparing and contrasting cases vs. controls; extracting variant or non-variant loci that meet certain requirements, displaying just a few samples in a browser like IGV, etc.). SelectVariants can be used for this purpose. Given a single VCF file, one or more samples can be extracted from the file (based on a complete sample name or a pattern match). Variants can be further selected by specifying criteria for inclusion, i.e. "DP &gt; 1000" (depth of coverage greater than 1000x), "AF &lt; 0.25" (sites with allele frequency less than 0.25). These JEXL expressions are documented in the `Using JEXL expressions section &lt;http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk&gt;`_. One can optionally include concordance or discordance tracks for use in selecting overlapping variants.
232
233 For more information on using the SelectVariants module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_variantutils_SelectVariants.html&gt;`_.
234
235 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
236
237 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
238
239 ------
240
241 **Inputs**
242
243 GenomeAnalysisTK: SelectVariants accepts a VCF input file.
244
245
246 **Outputs**
247
248 The output is in VCF format.
249
250
251 Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
252
253 -------
254
255 **Settings**::
256
257
258 out VCFWriter stdout File to which variants should be written
259 variant RodBinding[VariantContext] NA Input VCF file
260 concordance RodBinding[VariantContext] none Output variants that were also called in this comparison track
261 discordance RodBinding[VariantContext] none Output variants that were not called in this comparison track
262 exclude_sample_file Set[File] [] File containing a list of samples (one per line) to exclude. Can be specified multiple times
263 exclude_sample_name Set[String] [] Exclude genotypes from this sample. Can be specified multiple times
264 excludeFiltered boolean false Don't include filtered loci in the analysis
265 excludeNonVariants boolean false Don't include loci found to be non-variant after the subsetting procedure
266 keepIDs File NA Only emit sites whose ID is found in this file (one ID per line)
267 keepOriginalAC boolean false Don't update the AC, AF, or AN values in the INFO field after selecting
268 mendelianViolation Boolean false output mendelian violation sites only
269 mvq double 0.0 Minimum genotype QUAL score for each trio member required to accept a site as a violation
270 remove_fraction_genotypes double 0.0 Selects a fraction (a number between 0 and 1) of the total genotypes at random from the variant track and sets them to nocall
271 restrictAllelesTo NumberAlleleRestriction ALL Select only variants of a particular allelicity. Valid options are ALL (default), MULTIALLELIC or BIALLELIC
272 sample_expressions Set[String] NA Regular expression to select many samples from the ROD tracks provided. Can be specified multiple times
273 sample_file Set[File] NA File containing a list of samples (one per line) to include. Can be specified multiple times
274 sample_name Set[String] [] Include genotypes from this sample. Can be specified multiple times
275 select_expressions ArrayList[String] [] One or more criteria to use when selecting the data
276 select_random_fraction double 0.0 Selects a fraction (a number between 0 and 1) of the total variants at random from the variant track
277 select_random_number int 0 Selects a number of variants at random from the variant track
278 selectTypeToInclude List[Type] [] Select only a certain type of variants from the input file. Valid types are INDEL, SNP, MIXED, MNP, SYMBOLIC, NO_VARIATION. Can be specified multiple times
279
280 @CITATION_SECTION@
281 </help>
282 <expand macro="citations" />
283 </tool>