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comparison DumpSTR/dumpSTR.xml @ 0:ecf8c4f9f8ba draft

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"planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
author michal_klinka
date Sat, 23 Apr 2022 16:34:03 +0000
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children 8e8cf43f6836
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-1:000000000000 0:ecf8c4f9f8ba
1 <?xml version="1.0" ?>
2 <tool id="dumpSTR" name="DumpSTR" version="@tool_version@">
3 <description>DumpSTR filters VCF files with TR genotypes, performing call-level and locus-level filtering, and
4 outputs a filtered VCF file.
5 </description>
6
7 <macros>
8 <import>macros.xml</import>
9 </macros>
10
11 <expand macro="requirements"/>
12 <version_command>dumpSTR --version</version_command>
13 <command detect_errors="exit_code"><![CDATA[dumpSTR
14 ## h definition
15 #if $options.h:
16 -h
17 #end if
18 ## end h definition
19 ## vcf definition
20 #if $input_output.vcf:
21 --vcf $input_output.vcf
22 #end if
23 ## end vcf definition
24 ## out definition
25 #if $input_output.out:
26 --out $input_output.out
27 #end if
28 ## end out definition
29 ## zip definition
30 #if $input_output.zip:
31 --zip
32 #end if
33 ## end zip definition
34 ## vcftype definition
35 #if $input_output.vcftype:
36 --vcftype $input_output.vcftype
37 #end if
38 ## end vcftype definition
39 ## min_locus_callrate definition
40 #if $locus_level_filters__tool_agnostic_.min_locus_callrate:
41 --min-locus-callrate $locus_level_filters__tool_agnostic_.min_locus_callrate
42 #end if
43 ## end min_locus_callrate definition
44 ## min_locus_hwep definition
45 #if $locus_level_filters__tool_agnostic_.min_locus_hwep:
46 --min-locus-hwep $locus_level_filters__tool_agnostic_.min_locus_hwep
47 #end if
48 ## end min_locus_hwep definition
49 ## min_locus_het definition
50 #if $locus_level_filters__tool_agnostic_.min_locus_het:
51 --min-locus-het $locus_level_filters__tool_agnostic_.min_locus_het
52 #end if
53 ## end min_locus_het definition
54 ## max_locus_het definition
55 #if $locus_level_filters__tool_agnostic_.max_locus_het:
56 --max-locus-het $locus_level_filters__tool_agnostic_.max_locus_het
57 #end if
58 ## end max_locus_het definition
59 ## use_length definition
60 #if $locus_level_filters__tool_agnostic_.use_length:
61 --use-length
62 #end if
63 ## end use_length definition
64 ## filter_regions definition
65 #if $locus_level_filters__tool_agnostic_.filter_regions:
66 --filter-regions $locus_level_filters__tool_agnostic_.filter_regions
67 #end if
68 ## end filter_regions definition
69 ## filter_regions_names definition
70 #if $locus_level_filters__tool_agnostic_.filter_regions_names:
71 --filter-regions-names $locus_level_filters__tool_agnostic_.filter_regions_names
72 #end if
73 ## end filter_regions_names definition
74 ## filter_hrun definition
75 #if $locus_level_filters__tool_agnostic_.filter_hrun:
76 --filter-hrun
77 #end if
78 ## end filter_hrun definition
79 ## drop_filtered definition
80 #if $locus_level_filters__tool_agnostic_.drop_filtered:
81 --drop-filtered
82 #end if
83 ## end drop_filtered definition
84 ## hipstr_max_call_flank_indel definition
85 #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel:
86 --hipstr-max-call-flank-indel $call_level_filters_specific_to_hipstr_output.hipstr_max_call_flank_indel
87 #end if
88 ## end hipstr_max_call_flank_indel definition
89 ## hipstr_max_call_stutter definition
90 #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter:
91 --hipstr-max-call-stutter $call_level_filters_specific_to_hipstr_output.hipstr_max_call_stutter
92 #end if
93 ## end hipstr_max_call_stutter definition
94 ## hipstr_min_supp_reads definition
95 #if $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads:
96 --hipstr-min-supp-reads $call_level_filters_specific_to_hipstr_output.hipstr_min_supp_reads
97 #end if
98 ## end hipstr_min_supp_reads definition
99 ## hipstr_min_call_DP definition
100 #if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP:
101 --hipstr-min-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_min_call_DP
102 #end if
103 ## end hipstr_min_call_DP definition
104 ## hipstr_max_call_DP definition
105 #if $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP:
106 --hipstr-max-call-DP $call_level_filters_specific_to_hipstr_output.hipstr_max_call_DP
107 #end if
108 ## end hipstr_max_call_DP definition
109 ## hipstr_min_call_Q definition
110 #if $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q:
111 --hipstr-min-call-Q $call_level_filters_specific_to_hipstr_output.hipstr_min_call_Q
112 #end if
113 ## end hipstr_min_call_Q definition
114 ## gangstr_min_call_DP definition
115 #if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP:
116 --gangstr-min-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_min_call_DP
117 #end if
118 ## end gangstr_min_call_DP definition
119 ## gangstr_max_call_DP definition
120 #if $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP:
121 --gangstr-max-call-DP $call_level_filters_specific_to_gangstr_output.gangstr_max_call_DP
122 #end if
123 ## end gangstr_max_call_DP definition
124 ## gangstr_min_call_Q definition
125 #if $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q:
126 --gangstr-min-call-Q $call_level_filters_specific_to_gangstr_output.gangstr_min_call_Q
127 #end if
128 ## end gangstr_min_call_Q definition
129 ## gangstr_expansion_prob_het definition
130 #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het:
131 --gangstr-expansion-prob-het $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_het
132 #end if
133 ## end gangstr_expansion_prob_het definition
134 ## gangstr_expansion_prob_hom definition
135 #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom:
136 --gangstr-expansion-prob-hom $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_hom
137 #end if
138 ## end gangstr_expansion_prob_hom definition
139 ## gangstr_expansion_prob_total definition
140 #if $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total:
141 --gangstr-expansion-prob-total $call_level_filters_specific_to_gangstr_output.gangstr_expansion_prob_total
142 #end if
143 ## end gangstr_expansion_prob_total definition
144 ## gangstr_filter_span_only definition
145 #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_span_only:
146 --gangstr-filter-span-only
147 #end if
148 ## end gangstr_filter_span_only definition
149 ## gangstr_filter_spanbound_only definition
150 #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_spanbound_only:
151 --gangstr-filter-spanbound-only
152 #end if
153 ## end gangstr_filter_spanbound_only definition
154 ## gangstr_filter_badCI definition
155 #if $call_level_filters_specific_to_gangstr_output.gangstr_filter_badCI:
156 --gangstr-filter-badCI
157 #end if
158 ## end gangstr_filter_badCI definition
159 ## gangstr_readlen definition
160 #if $call_level_filters_specific_to_gangstr_output.gangstr_readlen:
161 --gangstr-readlen $call_level_filters_specific_to_gangstr_output.gangstr_readlen
162 #end if
163 ## end gangstr_readlen definition
164 ## advntr_min_call_DP definition
165 #if $call_level_filters_specific_to_advntr_output.advntr_min_call_DP:
166 --advntr-min-call-DP $call_level_filters_specific_to_advntr_output.advntr_min_call_DP
167 #end if
168 ## end advntr_min_call_DP definition
169 ## advntr_max_call_DP definition
170 #if $call_level_filters_specific_to_advntr_output.advntr_max_call_DP:
171 --advntr-max-call-DP $call_level_filters_specific_to_advntr_output.advntr_max_call_DP
172 #end if
173 ## end advntr_max_call_DP definition
174 ## advntr_min_spanning definition
175 #if $call_level_filters_specific_to_advntr_output.advntr_min_spanning:
176 --advntr-min-spanning $call_level_filters_specific_to_advntr_output.advntr_min_spanning
177 #end if
178 ## end advntr_min_spanning definition
179 ## advntr_min_flanking definition
180 #if $call_level_filters_specific_to_advntr_output.advntr_min_flanking:
181 --advntr-min-flanking $call_level_filters_specific_to_advntr_output.advntr_min_flanking
182 #end if
183 ## end advntr_min_flanking definition
184 ## advntr_min_ML definition
185 #if $call_level_filters_specific_to_advntr_output.advntr_min_ML:
186 --advntr-min-ML $call_level_filters_specific_to_advntr_output.advntr_min_ML
187 #end if
188 ## end advntr_min_ML definition
189 ## eh_min_ADFL definition
190 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL:
191 --eh-min-ADFL $call_level_filters_specific_to_expansionhunter_output.eh_min_ADFL
192 #end if
193 ## end eh_min_ADFL definition
194 ## eh_min_ADIR definition
195 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR:
196 --eh-min-ADIR $call_level_filters_specific_to_expansionhunter_output.eh_min_ADIR
197 #end if
198 ## end eh_min_ADIR definition
199 ## eh_min_ADSP definition
200 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP:
201 --eh-min-ADSP $call_level_filters_specific_to_expansionhunter_output.eh_min_ADSP
202 #end if
203 ## end eh_min_ADSP definition
204 ## eh_min_call_LC definition
205 #if $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC:
206 --eh-min-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_min_call_LC
207 #end if
208 ## end eh_min_call_LC definition
209 ## eh_max_call_LC definition
210 #if $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC:
211 --eh-max-call-LC $call_level_filters_specific_to_expansionhunter_output.eh_max_call_LC
212 #end if
213 ## end eh_max_call_LC definition
214 ## popstr_min_call_DP definition
215 #if $call_level_filters_specific_to_popstr_output.popstr_min_call_DP:
216 --popstr-min-call-DP $call_level_filters_specific_to_popstr_output.popstr_min_call_DP
217 #end if
218 ## end popstr_min_call_DP definition
219 ## popstr_max_call_DP definition
220 #if $call_level_filters_specific_to_popstr_output.popstr_max_call_DP:
221 --popstr-max-call-DP $call_level_filters_specific_to_popstr_output.popstr_max_call_DP
222 #end if
223 ## end popstr_max_call_DP definition
224 ## popstr_require_support definition
225 #if $call_level_filters_specific_to_popstr_output.popstr_require_support:
226 --popstr-require-support $call_level_filters_specific_to_popstr_output.popstr_require_support
227 #end if
228 ## end popstr_require_support definition
229 ## num_records definition
230 #if $debugging_parameters.num_records:
231 --num-records $debugging_parameters.num_records
232 #end if
233 ## end num_records definition
234 ## die_on_warning definition
235 #if $debugging_parameters.die_on_warning:
236 --die-on-warning
237 #end if
238 ## end die_on_warning definition
239 ## verbose definition
240 #if $debugging_parameters.verbose:
241 --verbose
242 #end if
243 ## end verbose definition
244 ## version definition
245 #if $version313f.version:
246 --version
247 #end if
248 ## end version definition
249 1>$stdout 2>$stderr
250 ]]></command>
251
252
253 <inputs>
254
255
256 <section name="options" title="options" expanded="false">
257 <param argument="-h" type="boolean" optional="true" label="help" help="show this help message and exit"/>
258 </section>
259 <section name="input_output" title="Input/output" expanded="false">
260 <param argument="--vcf" type="data" format="vcf" optional="false" label="vcf" help="Input STR VCF file"/>
261 <param argument="--out" type="text" optional="false" label="out" help="Prefix for output files"/>
262 <param argument="--zip" type="boolean" optional="true" label="zip"
263 help="Produce a bgzipped and tabix indexed output VCF"/>
264 <param argument="--vcftype" type="select" optional="true" label="vcftype"
265 help="Genotyper that was used to create this VCF input">
266 <expand macro="vcfTypes"/>
267 </param>
268 </section>
269 <section name="locus_level_filters__tool_agnostic_" title="Locus-level filters (tool agnostic)"
270 expanded="false">
271 <param argument="--min-locus-callrate" type="float" optional="true" label="min_locus_callrate"
272 help="Minimum locus call rate"/>
273 <param argument="--min-locus-hwep" type="float" optional="true" label="min_locus_hwep"
274 help="Filter loci failing HWE at this p-value threshold"/>
275 <param argument="--min-locus-het" type="float" optional="true" label="min_locus_het"
276 help="Minimum locus heterozygosity"/>
277 <param argument="--max-locus-het" type="float" optional="true" label="max_locus_het"
278 help="Maximum locus heterozygosity"/>
279 <param argument="--use-length" type="boolean" optional="true" label="use_length"
280 help="Calculate per-locus stats (het, HWE) collapsing alleles by length"/>
281 <param argument="--filter-regions" type="text" optional="true" label="filter_regions"
282 help="Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed"/>
283 <param argument="--filter-regions-names" type="text" optional="true" label="filter_regions_names"
284 help="Comma-separated list of filter names for each BED filter file"/>
285 <param argument="--filter-hrun" type="boolean" optional="true" label="filter_hrun"
286 help="Filter STRs with long homopolymer runs."/>
287 <param argument="--drop-filtered" type="boolean" optional="true" label="drop_filtered"
288 help="Drop filtered records from output"/>
289 </section>
290 <section name="call_level_filters_specific_to_hipstr_output"
291 title="Call-level filters specific to HipSTR output" expanded="false">
292 <param argument="--hipstr-max-call-flank-indel" type="float" optional="true"
293 label="hipstr_max_call_flank_indel" help="Maximum call flank indel rate"/>
294 <param argument="--hipstr-max-call-stutter" type="float" optional="true" label="hipstr_max_call_stutter"
295 help="Maximum call stutter rate"/>
296 <param argument="--hipstr-min-supp-reads" type="integer" optional="true" label="hipstr_min_supp_reads"
297 help="Minimum supporting reads for each allele"/>
298 <param argument="--hipstr-min-call-DP" type="integer" optional="true" label="hipstr_min_call_DP"
299 help="Minimum call coverage"/>
300 <param argument="--hipstr-max-call-DP" type="integer" optional="true" label="hipstr_max_call_DP"
301 help="Maximum call coverage"/>
302 <param argument="--hipstr-min-call-Q" type="float" optional="true" label="hipstr_min_call_Q"
303 help="Minimum call quality score"/>
304 </section>
305 <section name="call_level_filters_specific_to_gangstr_output"
306 title="Call-level filters specific to GangSTR output" expanded="false">
307 <param argument="--gangstr-min-call-DP" type="integer" optional="true" label="gangstr_min_call_DP"
308 help="Minimum call coverage"/>
309 <param argument="--gangstr-max-call-DP" type="integer" optional="true" label="gangstr_max_call_DP"
310 help="Maximum call coverage"/>
311 <param argument="--gangstr-min-call-Q" type="float" optional="true" label="gangstr_min_call_Q"
312 help="Minimum call quality score"/>
313 <param argument="--gangstr-expansion-prob-het" type="float" optional="true"
314 label="gangstr_expansion_prob_het"
315 help="Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less than this"/>
316 <param argument="--gangstr-expansion-prob-hom" type="float" optional="true"
317 label="gangstr_expansion_prob_hom"
318 help="Expansion prob-value threshold. Filters calls with probability of homozygous expansion less than this"/>
319 <param argument="--gangstr-expansion-prob-total" type="float" optional="true"
320 label="gangstr_expansion_prob_total"
321 help="Expansion prob-value threshold. Filters calls with probability of total expansion less than this"/>
322 <param argument="--gangstr-filter-span-only" type="boolean" optional="true" label="gangstr_filter_span_only"
323 help="Filter out all calls that only have spanning read support"/>
324 <param argument="--gangstr-filter-spanbound-only" type="boolean" optional="true"
325 label="gangstr_filter_spanbound_only" help="Filter out all reads except spanning and bounding"/>
326 <param argument="--gangstr-filter-badCI" type="boolean" optional="true" label="gangstr_filter_badCI"
327 help="Filter regions where the ML estimate is not in the CI"/>
328 <param argument="--gangstr-readlen" type="integer" optional="true" label="gangstr_readlen"
329 help="Read length used (bp). Required if using --require-support"/>
330 </section>
331 <section name="call_level_filters_specific_to_advntr_output"
332 title="Call-level filters specific to adVNTR output" expanded="false">
333 <param argument="--advntr-min-call-DP" type="integer" optional="true" label="advntr_min_call_DP"
334 help="Minimum call coverage"/>
335 <param argument="--advntr-max-call-DP" type="integer" optional="true" label="advntr_max_call_DP"
336 help="Maximum call coverage"/>
337 <param argument="--advntr-min-spanning" type="integer" optional="true" label="advntr_min_spanning"
338 help="Minimum spanning read count (SR field)"/>
339 <param argument="--advntr-min-flanking" type="integer" optional="true" label="advntr_min_flanking"
340 help="Minimum flanking read count (FR field)"/>
341 <param argument="--advntr-min-ML" type="float" optional="true" label="advntr_min_ML"
342 help="Minimum value of maximum likelihood (ML field)"/>
343 </section>
344 <section name="call_level_filters_specific_to_expansionhunter_output"
345 title="Call-level filters specific to ExpansionHunter output" expanded="false">
346 <param argument="--eh-min-ADFL" type="integer" optional="true" label="eh_min_ADFL"
347 help="Minimum number of flanking reads consistent with the allele"/>
348 <param argument="--eh-min-ADIR" type="integer" optional="true" label="eh_min_ADIR"
349 help="Minimum number of in-repeat reads consistent with the allele"/>
350 <param argument="--eh-min-ADSP" type="integer" optional="true" label="eh_min_ADSP"
351 help="Minimum number of spanning reads consistent with the allele"/>
352 <param argument="--eh-min-call-LC" type="integer" optional="true" label="eh_min_call_LC"
353 help="Minimum call coverage"/>
354 <param argument="--eh-max-call-LC" type="integer" optional="true" label="eh_max_call_LC"
355 help="Maximum call coverage"/>
356 </section>
357 <section name="call_level_filters_specific_to_popstr_output"
358 title="Call-level filters specific to PopSTR output" expanded="false">
359 <param argument="--popstr-min-call-DP" type="integer" optional="true" label="popstr_min_call_DP"
360 help="Minimum call coverage"/>
361 <param argument="--popstr-max-call-DP" type="integer" optional="true" label="popstr_max_call_DP"
362 help="Maximum call coverage"/>
363 <param argument="--popstr-require-support" type="integer" optional="true" label="popstr_require_support"
364 help="Require each allele call to have at least n supporting reads"/>
365 </section>
366 <section name="debugging_parameters" title="Debugging parameters" expanded="false">
367 <param argument="--num-records" type="integer" optional="true" label="num_records"
368 help="Only process this many records"/>
369 <param argument="--die-on-warning" type="boolean" optional="true" label="die_on_warning"
370 help="Quit if a record can't be parsed"/>
371 <param argument="--verbose" type="boolean" optional="true" label="verbose" help="Print out extra info"/>
372 </section>
373 <section name="version313f" title="Version" expanded="false">
374 <param argument="--version" type="boolean" optional="true" label="version"
375 help="show program's version number and exit"/>
376 </section>
377 </inputs>
378
379
380 <outputs>
381 <data name="stdout" label="STDOUT output" format="txt"/>
382
383 <data name="main_output" label="Main output">
384 <discover_datasets format="vcf" pattern="(?P&lt;designation&gt;.+)\.vcf" visible="true"
385 assign_primary_output="true"/>
386 <discover_datasets format="tabular" pattern="(?P&lt;designation&gt;.+)\.tab" visible="true"/>
387 </data>
388
389 <data name="stderr" label="STDERR output" format="txt">
390 <discover_datasets format="vcf_bgzip" pattern="(?P&lt;designation&gt;.+)\.vcf.gz" visible="true"/>
391 <discover_datasets format="tabix" pattern="(?P&lt;designation&gt;.+)\.vcf.gz.tbi" visible="true"/>
392 </data>
393
394 </outputs>
395
396
397 <tests>
398 <test>
399 <section name="main_params">
400 <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/>
401 <param name="out" value="test_result"/>
402 <param name="vcftype" value="hipstr"/>
403 <param name="zip" value="false"/>
404 </section>
405 <section name="filter_opt">
406 <param name="min_locus_callrate" value="0.1"/>
407 <param name="use_length" value="true"/>
408 <param name="drop_filtered" value="true"/>
409 </section>
410 <section name="filter_call_level">
411 <section name="hipstr_filters">
412 <param name="hipstr_max_call_flank_indel" value="0.2"/>
413 <param name="hipstr_min_call_Q" value="0.4"/>
414 </section>
415 </section>
416
417 <output name="stdout" file="stdout.txt"/>
418
419 <output name="main_output">
420 <discovered_dataset designation="test_result.loclog" file="test_result.loclog.tab"/>
421 <discovered_dataset designation="test_result.samplog" file="test_result.samplog.tab"/>
422 <discovered_dataset designation="test_result">
423 <assert_contents>
424 <has_size value="4061730" delta="200"/>
425 <has_text text="##fileformat=VCFv4.1"/>
426 <has_n_lines n="9046"/>
427 </assert_contents>
428 </discovered_dataset>
429 </output>
430 <output name="stderr" file="stderr.txt"/>
431
432 </test>
433 </tests>
434
435
436 <help>usage: main.py [-h] --vcf VCF --out OUT [--zip] [--vcftype VCFTYPE] [--min-locus-callrate MIN_LOCUS_CALLRATE]
437 [--min-locus-hwep MIN_LOCUS_HWEP] [--min-locus-het MIN_LOCUS_HET] [--max-locus-het MAX_LOCUS_HET] [--use-length]
438 [--filter-regions FILTER_REGIONS] [--filter-regions-names FILTER_REGIONS_NAMES] [--filter-hrun]
439 [--drop-filtered] [--hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL]
440 [--hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER] [--hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS]
441 [--hipstr-min-call-DP HIPSTR_MIN_CALL_DP] [--hipstr-max-call-DP HIPSTR_MAX_CALL_DP]
442 [--hipstr-min-call-Q HIPSTR_MIN_CALL_Q] [--gangstr-min-call-DP GANGSTR_MIN_CALL_DP] [--gangstr-max-call-DP
443 GANGSTR_MAX_CALL_DP] [--gangstr-min-call-Q GANGSTR_MIN_CALL_Q]
444 [--gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET] [--gangstr-expansion-prob-hom
445 GANGSTR_EXPANSION_PROB_HOM] [--gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL]
446 [--gangstr-filter-span-only]
447 [--gangstr-filter-spanbound-only] [--gangstr-filter-badCI] [--gangstr-readlen GANGSTR_READLEN]
448 [--advntr-min-call-DP ADVNTR_MIN_CALL_DP] [--advntr-max-call-DP ADVNTR_MAX_CALL_DP]
449 [--advntr-min-spanning ADVNTR_MIN_SPANNING] [--advntr-min-flanking ADVNTR_MIN_FLANKING] [--advntr-min-ML
450 ADVNTR_MIN_ML] [--eh-min-ADFL EH_MIN_ADFL] [--eh-min-ADIR EH_MIN_ADIR] [--eh-min-ADSP EH_MIN_ADSP]
451 [--eh-min-call-LC EH_MIN_CALL_LC] [--eh-max-call-LC EH_MAX_CALL_LC] [--popstr-min-call-DP POPSTR_MIN_CALL_DP]
452 [--popstr-max-call-DP POPSTR_MAX_CALL_DP] [--popstr-require-support POPSTR_REQUIRE_SUPPORT]
453 [--num-records NUM_RECORDS] [--die-on-warning] [--verbose] [--version]
454
455 options:
456 -h, --help show this help message and exit
457
458 Input/output:
459 --vcf VCF Input STR VCF file
460 --out OUT Prefix for output files
461 --zip Produce a bgzipped and tabix indexed output VCF
462 --vcftype VCFTYPE ##!!## Name trh could not be loaded
463
464 Locus-level filters (tool agnostic):
465 --min-locus-callrate MIN_LOCUS_CALLRATE
466 Minimum locus call rate
467 --min-locus-hwep MIN_LOCUS_HWEP
468 Filter loci failing HWE at this p-value threshold
469 --min-locus-het MIN_LOCUS_HET
470 Minimum locus heterozygosity
471 --max-locus-het MAX_LOCUS_HET
472 Maximum locus heterozygosity
473 --use-length Calculate per-locus stats (het, HWE) collapsing alleles by length
474 --filter-regions FILTER_REGIONS
475 Comma-separated list of BED files of regions to filter. Must be bgzipped and tabix indexed
476 --filter-regions-names FILTER_REGIONS_NAMES
477 Comma-separated list of filter names for each BED filter file
478 --filter-hrun Filter STRs with long homopolymer runs.
479 --drop-filtered Drop filtered records from output
480
481 Call-level filters specific to HipSTR output:
482 --hipstr-max-call-flank-indel HIPSTR_MAX_CALL_FLANK_INDEL
483 Maximum call flank indel rate
484 --hipstr-max-call-stutter HIPSTR_MAX_CALL_STUTTER
485 Maximum call stutter rate
486 --hipstr-min-supp-reads HIPSTR_MIN_SUPP_READS
487 Minimum supporting reads for each allele
488 --hipstr-min-call-DP HIPSTR_MIN_CALL_DP
489 Minimum call coverage
490 --hipstr-max-call-DP HIPSTR_MAX_CALL_DP
491 Maximum call coverage
492 --hipstr-min-call-Q HIPSTR_MIN_CALL_Q
493 Minimum call quality score
494
495 Call-level filters specific to GangSTR output:
496 --gangstr-min-call-DP GANGSTR_MIN_CALL_DP
497 Minimum call coverage
498 --gangstr-max-call-DP GANGSTR_MAX_CALL_DP
499 Maximum call coverage
500 --gangstr-min-call-Q GANGSTR_MIN_CALL_Q
501 Minimum call quality score
502 --gangstr-expansion-prob-het GANGSTR_EXPANSION_PROB_HET
503 Expansion prob-value threshold. Filters calls with probability of heterozygous expansion less than this
504 --gangstr-expansion-prob-hom GANGSTR_EXPANSION_PROB_HOM
505 Expansion prob-value threshold. Filters calls with probability of homozygous expansion less than this
506 --gangstr-expansion-prob-total GANGSTR_EXPANSION_PROB_TOTAL
507 Expansion prob-value threshold. Filters calls with probability of total expansion less than this
508 --gangstr-filter-span-only
509 Filter out all calls that only have spanning read support
510 --gangstr-filter-spanbound-only
511 Filter out all reads except spanning and bounding
512 --gangstr-filter-badCI
513 Filter regions where the ML estimate is not in the CI
514 --gangstr-readlen GANGSTR_READLEN
515 Read length used (bp). Required if using --require-support
516
517 Call-level filters specific to adVNTR output:
518 --advntr-min-call-DP ADVNTR_MIN_CALL_DP
519 Minimum call coverage
520 --advntr-max-call-DP ADVNTR_MAX_CALL_DP
521 Maximum call coverage
522 --advntr-min-spanning ADVNTR_MIN_SPANNING
523 Minimum spanning read count (SR field)
524 --advntr-min-flanking ADVNTR_MIN_FLANKING
525 Minimum flanking read count (FR field)
526 --advntr-min-ML ADVNTR_MIN_ML
527 Minimum value of maximum likelihood (ML field)
528
529 Call-level filters specific to ExpansionHunter output:
530 --eh-min-ADFL EH_MIN_ADFL
531 Minimum number of flanking reads consistent with the allele
532 --eh-min-ADIR EH_MIN_ADIR
533 Minimum number of in-repeat reads consistent with the allele
534 --eh-min-ADSP EH_MIN_ADSP
535 Minimum number of spanning reads consistent with the allele
536 --eh-min-call-LC EH_MIN_CALL_LC
537 Minimum call coverage
538 --eh-max-call-LC EH_MAX_CALL_LC
539 Maximum call coverage
540
541 Call-level filters specific to PopSTR output:
542 --popstr-min-call-DP POPSTR_MIN_CALL_DP
543 Minimum call coverage
544 --popstr-max-call-DP POPSTR_MAX_CALL_DP
545 Maximum call coverage
546 --popstr-require-support POPSTR_REQUIRE_SUPPORT
547 Require each allele call to have at least n supporting reads
548
549 Debugging parameters:
550 --num-records NUM_RECORDS
551 Only process this many records
552 --die-on-warning Quit if a record can't be parsed
553 --verbose Print out extra info
554
555 Version:
556 --version show program's version number and exit
557 </help>
558
559
560 <citations>
561 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,
562 author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek},
563 year = {2020},
564 title = {TRTools},
565 publisher = {GitHub},
566 journal = {GitHub repository},
567 url = {https://github.com/gymreklab/trtools},
568 }
569 </citation>
570 </citations>
571 </tool>