Mercurial > repos > iuc > bcftools_convert_to_vcf
comparison macros.xml @ 0:b068ef999550 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author | iuc |
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date | Wed, 06 Jul 2016 07:02:49 -0400 (2016-07-06) |
parents | |
children | b8926b599d45 |
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1 | |
2 <macros> | |
3 <token name="@VERSION@">1.3</token> | |
4 <xml name="stdio"> | |
5 <stdio> | |
6 <exit_code range="1:" /> | |
7 <exit_code range=":-1" /> | |
8 <regex match="Error:" /> | |
9 <regex match="Exception:" /> | |
10 </stdio> | |
11 </xml> | |
12 <xml name="requirements"> | |
13 <requirements> | |
14 <requirement type="package" version="1.3">bcftools</requirement> | |
15 <!-- conda dependency --> | |
16 <requirement type="package" version="1.3">htslib</requirement> | |
17 <requirement type="package" version="0.2.6">tabix</requirement> | |
18 <requirement type="package" version="1.2">samtools</requirement> | |
19 </requirements> | |
20 </xml> | |
21 <xml name="version_command"> | |
22 <version_command>bcftools 2>&1 | grep 'Version:'</version_command> | |
23 </xml> | |
24 | |
25 <xml name="citations"> | |
26 <citations> | |
27 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
28 <yield /> | |
29 </citations> | |
30 </xml> | |
31 <token name="@BCFTOOLS_WIKI@">https://github.com/samtools/bcftools/wiki</token> | |
32 <token name="@BCFTOOLS_MANPAGE@">http://samtools.github.io/bcftools/bcftools.html</token> | |
33 <token name="@THREADS@"> | |
34 --threads \${GALAXY_SLOTS:-4} | |
35 </token> | |
36 <token name="@PREPARE_ENV@"> | |
37 <![CDATA[ | |
38 export BCFTOOLS_PLUGINS=`which bcftools | sed 's,bin/bcftools,libexec/bcftools,'`; | |
39 ]]> | |
40 </token> | |
41 <xml name="macro_input"> | |
42 <param name="input_file" type="data" format="vcf,vcf_bgzip,bcf,bcf_bgzip" label="VCF/BCF Data" /> | |
43 </xml> | |
44 <token name="@PREPARE_INPUT_FILE@"> | |
45 <![CDATA[ | |
46 ## May need to symlink input if there is an associated | |
47 #set $input_vcf = 'input.vcf.gz' | |
48 #if $input_file.datatype.file_ext == 'vcf' | |
49 bgzip -c "$input_file" > $input_vcf && | |
50 bcftools index $input_vcf && | |
51 #elif $input_file.datatype.file_ext == 'vcf_bgzip' | |
52 ln -s "$input_file" $input_vcf | |
53 #elif $input_file.datatype.file_ext == 'bcf' | |
54 #set $input_vcf = 'input.bcf' | |
55 ln -s "$input_file" $input_vcf && | |
56 #if $input_file.metadata.bcf_index: | |
57 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && | |
58 #else | |
59 bcftools index $input_vcf && | |
60 #end if | |
61 #elif $input_file.datatype.file_ext == 'bcf_bgzip' | |
62 ln -s "$input_file" $input_vcf | |
63 #end if | |
64 ]]> | |
65 </token> | |
66 <token name="@INPUT_FILE@"> | |
67 $input_vcf | |
68 </token> | |
69 | |
70 <xml name="macro_inputs"> | |
71 <param name="input_files" type="data" format="vcf,bcf" label="Other VCF/BCF Datasets" multiple="True" /> | |
72 </xml> | |
73 <token name="@PREPARE_INPUT_FILES@"> | |
74 <![CDATA[ | |
75 ## May need to symlink input if there is an associated | |
76 #set $input_vcfs = [] | |
77 #set $vcfs_list_file = 'vcfs_list' | |
78 #for (i,input_file) in enumerate($input_files): | |
79 #set $input_vcf = 'input' + str($i) + '.vcf.gz' | |
80 echo '$input_vcf' >> $vcfs_list_file && | |
81 #if $input_file.datatype.file_ext == 'vcf' | |
82 bgzip -c "$input_file" > $input_vcf && | |
83 bcftools index $input_vcf && | |
84 #elif $input_file.datatype.file_ext == 'vcf_bgz' | |
85 ln -s "$input_file" $input_vcf | |
86 #elif $input_file.datatype.file_ext == 'bcf' | |
87 #set $input_vcf = 'input' + str($i) + '.bcf.gz' | |
88 ## bgzip -c "$input_file" > $input_vcf && | |
89 ln -s "$input_file" $input_vcf && | |
90 #if $input_file.metadata.bcf_index: | |
91 ln -s $input_file.metadata.bcf_index ${input_vcf}.csi && | |
92 #else | |
93 bcftools index $input_vcf && | |
94 #end if | |
95 #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' | |
96 ln -s "$input_file" $input_vcf && | |
97 #end if | |
98 $input_vcfs.append($input_vcf) | |
99 #end for | |
100 ]]> | |
101 </token> | |
102 <token name="@INPUT_FILES@"> | |
103 #echo ' '.join($input_vcfs)# | |
104 </token> | |
105 <token name="@INPUT_LIST_FILE@"> | |
106 $vcfs_list_file | |
107 </token> | |
108 | |
109 <xml name="macro_fasta_ref"> | |
110 <param name="fasta_ref" type="data" format="data" label="Fasta Ref" optional="True" help="reference sequence in fasta format" /> | |
111 </xml> | |
112 <token name="@PREPARE_FASTA_REF@"> | |
113 <![CDATA[ | |
114 #set $input_fa_ref = None | |
115 #if 'fasta_ref' in $section and $section.fasta_ref: | |
116 #set $input_fa_ref = 'ref.fa' | |
117 ln -s $section.fasta_ref $input_fa_ref && | |
118 samtools faidx $input_fa_ref && | |
119 #end if | |
120 ]]> | |
121 </token> | |
122 <token name="@FASTA_REF@"> | |
123 #if $input_fa_ref is not None: | |
124 --fasta-ref "$input_fa_ref" | |
125 #elif 'fasta_ref' in $section and $section.fasta_ref: | |
126 --fasta-ref "${section.fasta_ref}" | |
127 #end if | |
128 </token> | |
129 | |
130 <xml name="macro_ref_fasta"> | |
131 <conditional name="reference_source"> | |
132 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> | |
133 <option value="cached">Locally cached</option> | |
134 <option value="history">History</option> | |
135 </param> | |
136 <when value="cached"> | |
137 <param name="ref_file" type="select" label="Select reference genome"> | |
138 <options from_data_table="fasta_indexes"> | |
139 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>--> | |
140 </options> | |
141 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> | |
142 </param> | |
143 </when> | |
144 <when value="history"> <!-- FIX ME!!!! --> | |
145 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> | |
146 </when> | |
147 </conditional> | |
148 </xml> | |
149 | |
150 | |
151 <xml name="macro_AF_file"> | |
152 <param name="AF_file" type="data" format="data" label="Af File" optional="True" help="read allele frequencies from file (CHR\tPOS\tREF,ALT\tAF)" /> | |
153 </xml> | |
154 <!-- This may need to bgzip and tabix the file --> | |
155 <token name="@PREPARE_AF_FILE@"> | |
156 <![CDATA[ | |
157 #if 'AF_file' in $section and $section.AF_file: | |
158 #pass | |
159 #end if | |
160 ]]> | |
161 </token> | |
162 <token name="@AF_FILE@"> | |
163 #if 'AF_file' in $section and $section.AF_file: | |
164 --AF-file "${section.AF_file}" | |
165 #end if | |
166 </token> | |
167 | |
168 <xml name="macro_estimate_AF"> | |
169 <param name="estimate_AF" type="data" format="data" label="Estimate Af" optional="True" help="calculate AC,AN counts on the fly, using either all samples ("-") or samples listed in <file>" /> | |
170 </xml> | |
171 <token name="@ESTIMATE_AF@"> | |
172 #if 'estimate_AF' in $section and $section.estimate_AF: | |
173 --estimate-AF "${section.estimate_AF}" | |
174 #end if | |
175 </token> | |
176 | |
177 <xml name="macro_exons_file"> | |
178 <param name="exons_file" type="data" format="tabular" label="exons file" optional="True" help="tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)" /> | |
179 </xml> | |
180 <token name="@PREPARE_EXONS_FILE@"> | |
181 <![CDATA[ | |
182 #set $exons_path = None | |
183 #if 'exons_file' in $section and $section.exons_file: | |
184 #set $exons_path = 'exons_file.tab.gz' | |
185 bgzip -c "$section.exons_file" > $exons_path && | |
186 tabix -s 1 -b 2 -e 3 $exons_path && | |
187 #end if | |
188 ]]> | |
189 </token> | |
190 <token name="@EXONS_FILE@"> | |
191 #if 'exons_file' in $section and $section.exons_file: | |
192 --exons $exons_path | |
193 #end if | |
194 </token> | |
195 | |
196 <xml name="macro_ploidy_file"> | |
197 <param name="ploidy_file" type="data" format="tabular" label="Ploidy file" optional="True" help="tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> | |
198 </xml> | |
199 <token name="@PLOIDY_FILE@"> | |
200 #if 'ploidy_file' in $section and $section.ploidy_file: | |
201 --ploidy "${section.ploidy_file}" | |
202 #end if | |
203 </token> | |
204 | |
205 <xml name="macro_collapse_opt_none"> | |
206 <option value="none">none - require the exact same set of alleles in all files</option> | |
207 </xml> | |
208 <xml name="macro_collapse_opt_id"> | |
209 <option value="id">id - only records with identical ID column are compatible. </option> | |
210 </xml> | |
211 <xml name="macro_collapse"> | |
212 <param name="collapse" type="select" label="Collapse" optional="True" help="Controls how to treat records with duplicate positions and defines compatible records across multiple input files"> | |
213 <option value="snps">snps - allow different alleles, as long as they all are SNPs</option> | |
214 <option value="indels">indels - allow different alleles, as long as they all are indels</option> | |
215 <option value="both">both - indels and snps </option> | |
216 <option value="some">some - at least some of the ALTs must match</option> | |
217 <option value="any">any - any combination of alleles</option> | |
218 <yield/> | |
219 </param> | |
220 </xml> | |
221 <token name="@COLLAPSE@"> | |
222 #if $section.collapse: | |
223 --collapse "${section.collapse}" | |
224 #end if | |
225 </token> | |
226 | |
227 <xml name="macro_apply_filters"> | |
228 <param name="apply_filters" type="text" value="" label="Apply Filters" optional="true" | |
229 help="(-f --apply-filters) Skip sites where FILTER column does not contain any of the strings listed (e.g. "PASS,.")"> | |
230 <validator type="regex" message="FILTER terms separated by commas">^([^ \t\n\r\f\v,]+(,[^ \t\n\r\f\v,]+)*)?$</validator> | |
231 </param> | |
232 </xml> | |
233 <token name="@APPLY_FILTERS@"> | |
234 #if $section.apply_filters: | |
235 --apply-filters "${section.apply_filters}" | |
236 #end if | |
237 </token> | |
238 | |
239 <xml name="macro_select_output_type"> | |
240 <param name="output_type" type="select"> | |
241 <option value="b">compressed BCF</option> | |
242 <!-- no galaxy datatypes for these | |
243 <option value="u">uncompressed BCF</option> | |
244 <option value="z">compressed VCF</option> | |
245 --> | |
246 <option value="v">uncompressed VCF</option> | |
247 </param> | |
248 </xml> | |
249 <token name="@OUTPUT_TYPE@"> | |
250 #if str($output_type) != "__none__": | |
251 --output-type "${output_type}" | |
252 #end if | |
253 </token> | |
254 | |
255 <xml name="macro_vcf_output"> | |
256 <data name="output_file" format="vcf"> | |
257 <change_format> | |
258 <when input="output_type" value="b" format="bcf" /> | |
259 <when input="output_type" value="u" format="bcf" /> | |
260 <when input="output_type" value="z" format="vcf_bgzip" /> | |
261 <when input="output_type" value="v" format="vcf" /> | |
262 </change_format> | |
263 </data> | |
264 </xml> | |
265 | |
266 <xml name="macro_regions"> | |
267 <conditional name="regions"> | |
268 <param name="regions_src" type="select" label="Regions"> | |
269 <option value="__none__">None</option> | |
270 <option value="regions">regions</option> | |
271 <option value="regions_file">regions-file</option> | |
272 </param> | |
273 <when value="__none__"/> | |
274 <when value="regions"> | |
275 <param name="regions" type="text" value="" label="restrict to comma-separated list of regions" optional="true" | |
276 help="Each region is specifed as: chr or chr:pos or chr:from-to"> | |
277 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> | |
278 </param> | |
279 </when> | |
280 <when value="regions_file"> | |
281 <param name="regions_file" type="data" format="vcf,bed,tabular" label="Regions File" optional="True" help="restrict to regions listed in a file" /> | |
282 </when> | |
283 </conditional> | |
284 </xml> | |
285 <token name="@REGIONS@"> | |
286 #if $section.regions.regions_src == 'regions' and $section.regions.regions != '': | |
287 --regions "$section.regions.regions" | |
288 #elif $section.regions.regions_src == 'regions_file' and $section.regions.regions_file: | |
289 --regions-file "$section.regions.regions_file" | |
290 #end if | |
291 </token> | |
292 | |
293 <xml name="macro_targets_file"> | |
294 <param name="targets_file" type="data" format="tabular" label="Targets File" help="restrict to targets listed in a file" > | |
295 <yield/> | |
296 </param> | |
297 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the target file selection" /> | |
298 </xml> | |
299 <token name="@PREPARE_TARGETS_FILE@"> | |
300 <![CDATA[ | |
301 #set $targets_path = None | |
302 #if 'targets' in $section | |
303 #if $section.targets.targets_src == 'targets_file': | |
304 #set $targets_path = 'targets_file.tab.gz' | |
305 bgzip -c "$section.targets.targets_file" > $targets_path && | |
306 tabix -s 1 -b 2 -e 2 $targets_path && | |
307 #end if | |
308 #elif $tgts_sec.targets_file: | |
309 #set $targets_path = 'targets_file.tab.gz' | |
310 bgzip -c "$section.targets_file" > $targets_path && | |
311 tabix -s 1 -b 2 -e 2 $targets_path && | |
312 #end if | |
313 ]]> | |
314 </token> | |
315 <token name="@TARGETS_FILE@"> | |
316 <![CDATA[ | |
317 #if $targets_path is not None: | |
318 --targets-file "${section.invert_targets_file}${targets_path}" | |
319 #elif $section.targets_file: | |
320 --targets-file "${section.invert_targets_file}${section.targets_file}" | |
321 #end if | |
322 ]]> | |
323 </token> | |
324 | |
325 <xml name="macro_targets"> | |
326 <conditional name="targets"> | |
327 <param name="targets_src" type="select" label="Targets"> | |
328 <option value="__none__">None</option> | |
329 <option value="targets">targets</option> | |
330 <option value="targets_file">targets-file</option> | |
331 </param> | |
332 <when value="__none__"/> | |
333 <when value="targets"> | |
334 <param name="targets" type="text" value="" label="Restrict to comma-separated list of targets" optional="true" | |
335 help="Each target is specifed as: chr or chr:pos or chr:from-to"> | |
336 <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> | |
337 </param> | |
338 <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets" help="inverts the query/filtering applied by the targets" /> | |
339 </when> | |
340 <when value="targets_file"> | |
341 <expand macro="macro_targets_file"> | |
342 <optional>true</optional> | |
343 </expand> | |
344 </when> | |
345 </conditional> | |
346 </xml> | |
347 <token name="@TARGETS@"> | |
348 <![CDATA[ | |
349 #if $targets_path: | |
350 --targets-file "${section.targets.invert_targets_file}${targets_path}" | |
351 #else: | |
352 #if $section.targets.targets_src == 'targets' and $section.targets.targets != '': | |
353 --targets "${section.targets.invert_targets_file}${section.targets.targets}" | |
354 #elif $section.targets.targets_src == 'targets_file' and $section.targets.targets_file: | |
355 --targets-file "${section.targets.invert_targets_file}${section.targets.targets_file}" | |
356 #end if | |
357 #end if | |
358 ]]> | |
359 </token> | |
360 | |
361 <xml name="macro_samples"> | |
362 <param name="samples" type="text" value="" label="Samples" optional="true" | |
363 help="(-s) comma separated list of samples to annotate (or exclude with "^" prefix)"> | |
364 <validator type="regex" message="">^(\w+(,\w+)*)?$</validator> | |
365 </param> | |
366 <param name="invert_samples" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples" | |
367 help="inverts the query/filtering applied by Samples" /> | |
368 <param name="samples_file" type="data" format="tabular" label="Samples File" optional="True" | |
369 help="(-S) file of samples to include" /> | |
370 <param name="invert_samples_file" type="boolean" truevalue="^" falsevalue="" checked="false" label="Invert Samples File" | |
371 help="inverts the query/filtering applied by Samples File" /> | |
372 </xml> | |
373 <token name="@SAMPLES@"> | |
374 #set $samples_defined = False | |
375 #if str($section.samples) != '': | |
376 #set $samples_defined = True | |
377 --samples "${section.invert_samples}${section.samples}" | |
378 #end if | |
379 #if $section.samples_file: | |
380 #set $samples_defined = True | |
381 --samples-file "${section.invert_samples_file}${section.samples_file}" | |
382 #end if | |
383 </token> | |
384 | |
385 <xml name="macro_sample"> | |
386 <param name="sample" type="text" label="Sample" optional="True" help="apply variants of the given sample" /> | |
387 </xml> | |
388 <token name="@SAMPLE@"> | |
389 #if $section.sample: | |
390 --sample "${section.sample}" | |
391 #end if | |
392 </token> | |
393 | |
394 | |
395 <xml name="macro_include"> | |
396 <param name="include" type="text" label="Include" optional="True" help="(-i) select sites for which the expression is true"> | |
397 <validator type="regex" message="Single quote not allowed">^[^']*$</validator> | |
398 <sanitizer sanitize="False"/> | |
399 </param> | |
400 </xml> | |
401 <token name="@INCLUDE@"> | |
402 #if $section.include: | |
403 --include '${section.include}' | |
404 #end if | |
405 </token> | |
406 | |
407 <xml name="macro_exclude"> | |
408 <param name="exclude" type="text" label="Exclude" optional="True" help="(-e) exclude sites for which the expression is true"> | |
409 <validator type="regex" message="Single quote not allowed">^[^']*$</validator> | |
410 <sanitizer sanitize="False"/> | |
411 </param> | |
412 </xml> | |
413 <token name="@EXCLUDE@"> | |
414 #if $section.exclude: | |
415 --exclude '${section.exclude}' | |
416 #end if | |
417 </token> | |
418 | |
419 <xml name="macro_columns"> | |
420 <param name="columns" type="text" value="" label="Columns" optional="true" | |
421 help="list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details"> | |
422 <validator type="regex" message="COLUMN names separated by commas">^([^,]+(,[^,]+)*)?$</validator> | |
423 </param> | |
424 </xml> | |
425 <token name="@COLUMNS@"> | |
426 #if $section.columns != '': | |
427 --columns "${section.columns}" | |
428 #end if | |
429 </token> | |
430 | |
431 <xml name="macro_haploid2diploid"> | |
432 <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" label="Haploid2Diploid" help="convert haploid genotypes to diploid homozygotes" /> | |
433 </xml> | |
434 | |
435 <xml name="macro_vcf_ids"> | |
436 <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" label="Vcf Ids" help="output VCF IDs instead of CHROM:POS_REF_ALT" /> | |
437 </xml> | |
438 <token name="@VCF_IDS@"> | |
439 ${section.vcf_ids} | |
440 </token> | |
441 | |
442 <token name="@OUTPUT_HELP@"> | |
443 <![CDATA[ | |
444 Output Type | |
445 ----------- | |
446 | |
447 Output compressed BCF (b), or uncompressed VCF (v). | |
448 Use the BCF option when piping between bcftools subcommands to speed up | |
449 performance by removing unecessary compression/decompression | |
450 and VCF<->BCF conversion. | |
451 | |
452 This Galaxy tool recommends using the compressed BCF format | |
453 as piping is not implemented, and uncompressed data would | |
454 use unnecessary amounts of space. | |
455 | |
456 ]]></token> | |
457 <token name="@REGIONS_HELP@"> | |
458 <![CDATA[ | |
459 Region Selections | |
460 ----------------- | |
461 | |
462 Regions can be specified in a VCF, | |
463 BED, or tab-delimited file (the default). The columns of the | |
464 tab-delimited file are: CHROM, POS, and, optionally, POS_TO, | |
465 where positions are 1-based and inclusive. Uncompressed | |
466 files are stored in memory, while bgzip-compressed and | |
467 tabix-indexed region files are streamed. Note that sequence | |
468 names must match exactly, "chr20" is not the same as "20". | |
469 Also note that chromosome ordering in FILE will be | |
470 respected, the VCF will be processed in the order in which | |
471 chromosomes first appear in FILE. However, within | |
472 chromosomes, the VCF will always be processed in ascending | |
473 genomic coordinate order no matter what order they appear in | |
474 FILE. Note that overlapping regions in FILE can result in | |
475 duplicated out of order positions in the output. This option | |
476 requires indexed VCF/BCF files. | |
477 | |
478 ]]></token> | |
479 <token name="@TARGETS_HELP@"><![CDATA[ | |
480 Targets | |
481 ------- | |
482 | |
483 Similar to regions, but the next position is accessed by streaming the whole | |
484 VCF/BCF rather than using the tbi/csi index. Both regions and targets options can be | |
485 applied simultaneously: regions uses the index to jump to a region and targets discards | |
486 positions which are not in the targets. Unlike regions, targets can be prefixed with | |
487 "^" to request logical complement. For example, "^X,Y,MT" indicates that | |
488 sequences X, Y and MT should be skipped. Yet another difference between the two | |
489 is that regions checks both start and end positions of indels, whereas targets checks | |
490 start positions only. | |
491 | |
492 For the bcftools call command, with the option -C alleles, third column of the | |
493 targets file must be comma-separated list of alleles, starting with the | |
494 reference allele. Note that the file must be compressed and index. Such a file | |
495 can be easily created from a VCF using:: | |
496 | |
497 bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz | |
498 ]]> | |
499 <!-- TODO: galaxy-ify --> | |
500 </token> | |
501 | |
502 | |
503 <token name="@COLLAPSE_HELP@"> | |
504 Collapse | |
505 -------- | |
506 | |
507 Controls how to treat records with duplicate positions and defines compatible | |
508 records across multiple input files. Here by "compatible" we mean records which | |
509 should be considered as identical by the tools. For example, when performing | |
510 line intersections, the desire may be to consider as identical all sites with | |
511 matching positions (bcftools isec -c all), or only sites with matching variant | |
512 type (bcftools isec -c snps -c indels), or only sites with all alleles | |
513 identical (bcftools isec -c none). | |
514 | |
515 | |
516 +------------+----------------------------------------------------------------+ | |
517 | Flag value | Result | | |
518 +============+================================================================+ | |
519 | none | only records with identical REF and ALT alleles are compatible | | |
520 +------------+----------------------------------------------------------------+ | |
521 | some | only records where some subset of ALT alleles match are | | |
522 | | compatible | | |
523 +------------+----------------------------------------------------------------+ | |
524 | all | all records are compatible, regardless of whether the ALT | | |
525 | | alleles match or not. In the case of records with the same | | |
526 | | position, only the first wil lbe considered and appear on | | |
527 | | output. | | |
528 +------------+----------------------------------------------------------------+ | |
529 | snps | any SNP records are compatible, regardless of whether the ALT | | |
530 | | alleles match or not. For duplicate positions, only the first | | |
531 | | SNP record will be considered and appear on output. | | |
532 +------------+----------------------------------------------------------------+ | |
533 | indels | all indel records are compatible, regardless of whether the | | |
534 | | REF and ALT alleles match or not. For duplicate positions, | | |
535 | | only the first indel record will be considered and appear on | | |
536 | | output. | | |
537 +------------+----------------------------------------------------------------+ | |
538 | both | abbreviation of "-c indels -c snps" | | |
539 +------------+----------------------------------------------------------------+ | |
540 | id | only records with identical ID column are compatible. | | |
541 | | Supportedby bcftools merge only. | | |
542 +------------+----------------------------------------------------------------+ | |
543 | |
544 </token> | |
545 | |
546 <token name="@EXPRESSIONS_HELP@"> | |
547 <![CDATA[ | |
548 Expressions | |
549 ----------- | |
550 | |
551 Valid expressions may contain: | |
552 | |
553 - numerical constants, string constants | |
554 | |
555 :: | |
556 | |
557 1, 1.0, 1e-4 | |
558 "String" | |
559 | |
560 - arithmetic operators | |
561 | |
562 :: | |
563 | |
564 +,*,-,/ | |
565 | |
566 - comparison operators | |
567 | |
568 :: | |
569 | |
570 == (same as =), >, >=, <=, <, != | |
571 | |
572 - regex operators "~" and its negation "!~" | |
573 | |
574 :: | |
575 | |
576 INFO/HAYSTACK ~ "needle" | |
577 | |
578 - parentheses | |
579 | |
580 :: | |
581 | |
582 (, ) | |
583 | |
584 - logical operators | |
585 | |
586 :: | |
587 | |
588 && (same as &), ||, | | |
589 | |
590 - INFO tags, FORMAT tags, column names | |
591 | |
592 :: | |
593 | |
594 INFO/DP or DP | |
595 FORMAT/DV, FMT/DV, or DV | |
596 FILTER, QUAL, ID, REF, ALT[0] | |
597 | |
598 - 1 (or 0) to test the presence (or absence) of a flag | |
599 | |
600 :: | |
601 | |
602 FlagA=1 && FlagB=0 | |
603 | |
604 - "." to test missing values | |
605 | |
606 :: | |
607 | |
608 DP=".", DP!=".", ALT="." | |
609 | |
610 - missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".") using this expression | |
611 | |
612 :: | |
613 | |
614 GT="." | |
615 | |
616 - TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other) | |
617 | |
618 :: | |
619 | |
620 TYPE="indel" | TYPE="snp" | |
621 | |
622 - array subscripts, "*" for any field | |
623 | |
624 :: | |
625 | |
626 (DP4[0]+DP4[1])/(DP4[2]+DP4[3]) > 0.3 | |
627 DP4[*] == 0 | |
628 CSQ[*] ~ "missense_variant.*deleterious" | |
629 | |
630 - function on FORMAT tags (over samples) and INFO tags (over vector fields) | |
631 | |
632 :: | |
633 | |
634 MAX, MIN, AVG, SUM, STRLEN, ABS | |
635 | |
636 - variables calculated on the fly if not present: number of alternate alleles; number of samples; count of alternate alleles; minor allele count (similar to AC but is always smaller than 0.5); frequency of alternate alleles (AF=AC/AN); frequency of minor alleles (MAF=MAC/AN); number of alleles in called genotypes | |
637 | |
638 :: | |
639 | |
640 N_ALT, N_SAMPLES, AC, MAC, AF, MAF, AN | |
641 | |
642 **Notes:** | |
643 | |
644 - String comparisons and regular expressions are case-insensitive | |
645 - If the subscript "*" is used in regular expression search, the whole field | |
646 is treated as one string. For example, the regex ``STR[*]~"B,C"`` will be | |
647 true for the string vector INFO/STR=AB,CD. | |
648 - Variables and function names are case-insensitive, but not tag names. For | |
649 example, "qual" can be used instead of "QUAL", "strlen()" instead of | |
650 "STRLEN()" , but not "dp" instead of "DP". | |
651 | |
652 **Examples:** | |
653 | |
654 :: | |
655 | |
656 MIN(DV)>5 | |
657 MIN(DV/DP)>0.3 | |
658 MIN(DP)>10 & MIN(DV)>3 | |
659 FMT/DP>10 & FMT/GQ>10 .. both conditions must be satisfied within one sample | |
660 FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples | |
661 QUAL>10 | FMT/GQ>10 .. selects only GQ>10 samples | |
662 QUAL>10 || FMT/GQ>10 .. selects all samples at QUAL>10 sites | |
663 TYPE="snp" && QUAL>=10 && (DP4[2]+DP4[3] > 2) | |
664 MIN(DP)>35 && AVG(GQ)>50 | |
665 ID=@file .. selects lines with ID present in the file | |
666 ID!=@~/file .. skip lines with ID present in the ~/file | |
667 MAF[0]<0.05 .. select rare variants at 5% cutoff | |
668 | |
669 ]]></token> | |
670 | |
671 | |
672 | |
673 | |
674 </macros> |