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comparison tools/samtools/pileup_parser.xml @ 0:9071e359b9a3

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date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="pileup_parser" name="Filter pileup" version="1.0.2">>
2 <description>on coverage and SNPs</description>
3 <command interpreter="perl">
4 #if $pileup_type.type_select == "six" #pileup_parser.pl $input "3" "5" "6" "4" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
5 #elif $pileup_type.type_select == "ten" #pileup_parser.pl $input "3" "9" "10" "8" $qv_cutoff $cvrg_cutoff $snps_only $interval "2" $out_file1 $diff $qc_base
6 #elif $pileup_type.type_select == "manual" #pileup_parser.pl $input $pileup_type.ref_base_column $pileup_type.read_bases_column $pileup_type.read_qv_column $pileup_type.cvrg_column $qv_cutoff $cvrg_cutoff $snps_only $interval $pileup_type.coord_column $out_file1 $diff $qc_base
7 #end if#
8 </command>
9 <inputs>
10 <param name="input" type="data" format="tabular" label="Select dataset"/>
11 <conditional name="pileup_type">
12 <param name="type_select" type="select" label="which contains" help="See &quot;Types of pileup datasets&quot; below for examples">
13 <option value="six" selected="true">Pileup with six columns (simple)</option>
14 <option value="ten">Pileup with ten columns (with consensus)</option>
15 <option value="manual">Set columns manually</option>
16 </param>
17 <when value="manual">
18 <param name="ref_base_column" label="Select column with reference base" type="data_column" numerical="false" data_ref="input" />
19 <param name="read_bases_column" label="Select column with read bases" type="data_column" numerical="false" data_ref="input" help="something like this: ..,a.."/>
20 <param name="read_qv_column" label="Select column with base qualities" type="data_column" numerical="false" data_ref="input" help="something like this: IIIGIAI"/>
21 <param name="cvrg_column" label="Select column with coverage" type="data_column" numerical="true" data_ref="input" />
22 <param name="coord_column" label="Select coordinate column" type="data_column" numerical="true" data_ref="input" />
23 </when>
24 <when value="six">
25 </when>
26 <when value="ten">
27 </when>
28 </conditional>
29 <param name="qv_cutoff" label="Do not consider read bases with quality lower than" type="integer" value="20" help="No variants with quality below this value will be reported"/>
30 <param name="cvrg_cutoff" label="Do not report positions with coverage lower than" type="integer" value="3" help="Pileup lines with coverage lower than this value will be skipped"/>
31 <param name="snps_only" label="Only report variants?" type="select" help="See &quot;Examples 1 and 2&quot; below for explanation">
32 <option value="No">No</option>
33 <option value="Yes" selected="true">Yes</option>
34 </param>
35 <param name="interval" label="Convert coordinates to intervals?" type="select" help="See &quot;Output format&quot; below for explanation">
36 <option value="No" selected="true">No</option>
37 <option value="Yes">Yes</option>
38 </param>
39 <param name="diff" label="Print total number of differences?" type="select" help="See &quot;Example 3&quot; below for explanation">
40 <option value="No" selected="true">No</option>
41 <option value="Yes">Yes</option>
42 </param>
43 <param name="qc_base" label="Print quality and base string?" type="select" help="See &quot;Example 4&quot; below for explanation">
44 <option value="No">No</option>
45 <option value="Yes" selected="true">Yes</option>
46 </param>
47
48 </inputs>
49 <outputs>
50 <data format="tabular" name="out_file1">
51 <change_format>
52 <when input="interval" value="Yes" format="interval" />
53 </change_format>
54 </data>
55 </outputs>
56 <tests>
57 <test>
58 <param name="input" value="pileup_parser.6col.pileup"/>
59 <output name="out_file1" file="pileup_parser.6col.20-3-yes-yes.pileup.out"/>
60 <param name="type_select" value="six"/>
61 <param name="qv_cutoff" value="20" />
62 <param name="cvrg_cutoff" value="3" />
63 <param name="snps_only" value="Yes"/>
64 <param name="interval" value="Yes" />
65 <param name="diff" value="No" />
66 <param name="qc_base" value="Yes" />
67 </test>
68 <test>
69 <param name="input" value="pileup_parser.6col.pileup"/>
70 <output name="out_file1" file="pileup_parser.6col.20-3-yes-no.pileup.out"/>
71 <param name="type_select" value="six"/>
72 <param name="qv_cutoff" value="20" />
73 <param name="cvrg_cutoff" value="3" />
74 <param name="snps_only" value="Yes"/>
75 <param name="interval" value="No" />
76 <param name="diff" value="No" />
77 <param name="qc_base" value="Yes" />
78 </test>
79 <test>
80 <param name="input" value="pileup_parser.6col.pileup"/>
81 <output name="out_file1" file="pileup_parser.6col.20-3-no-no.pileup.out"/>
82 <param name="type_select" value="six"/>
83 <param name="qv_cutoff" value="20" />
84 <param name="cvrg_cutoff" value="3" />
85 <param name="snps_only" value="No"/>
86 <param name="interval" value="No" />
87 <param name="diff" value="No" />
88 <param name="qc_base" value="Yes" />
89 </test>
90 <test>
91 <param name="input" value="pileup_parser.10col.pileup"/>
92 <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/>
93 <param name="type_select" value="ten"/>
94 <param name="qv_cutoff" value="20" />
95 <param name="cvrg_cutoff" value="3" />
96 <param name="snps_only" value="Yes"/>q
97 <param name="interval" value="Yes" />
98 <param name="diff" value="No" />
99 <param name="qc_base" value="Yes" />
100 </test>
101 <test>
102 <param name="input" value="pileup_parser.10col.pileup"/>
103 <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes.pileup.out"/>
104 <param name="type_select" value="manual"/>
105 <param name="ref_base_column" value="3"/>
106 <param name="read_bases_column" value="9"/>
107 <param name="read_qv_column" value="10"/>
108 <param name="cvrg_column" value="8"/>
109 <param name="coord_column" value="2"/>
110 <param name="qv_cutoff" value="20" />
111 <param name="cvrg_cutoff" value="3" />
112 <param name="snps_only" value="Yes"/>
113 <param name="interval" value="Yes" />
114 <param name="diff" value="No" />
115 <param name="qc_base" value="Yes" />
116 </test>
117 <test>
118 <param name="input" value="pileup_parser.10col.pileup"/>
119 <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-yes.pileup.out"/>
120 <param name="type_select" value="manual"/>
121 <param name="ref_base_column" value="3"/>
122 <param name="read_bases_column" value="9"/>
123 <param name="read_qv_column" value="10"/>
124 <param name="cvrg_column" value="8"/>
125 <param name="coord_column" value="2"/>
126 <param name="qv_cutoff" value="20" />
127 <param name="cvrg_cutoff" value="3" />
128 <param name="snps_only" value="Yes"/>
129 <param name="interval" value="Yes" />
130 <param name="diff" value="Yes" />
131 <param name="qc_base" value="Yes" />
132 </test>
133 <test>
134 <param name="input" value="pileup_parser.10col.pileup"/>
135 <output name="out_file1" file="pileup_parser.10col.20-3-yes-yes-yes-no.pileup.out"/>
136 <param name="type_select" value="manual"/>
137 <param name="ref_base_column" value="3"/>
138 <param name="read_bases_column" value="9"/>
139 <param name="read_qv_column" value="10"/>
140 <param name="cvrg_column" value="8"/>
141 <param name="coord_column" value="2"/>
142 <param name="qv_cutoff" value="20" />
143 <param name="cvrg_cutoff" value="3" />
144 <param name="snps_only" value="Yes"/>
145 <param name="interval" value="Yes" />
146 <param name="diff" value="Yes" />
147 <param name="qc_base" value="No" />
148 </test>
149
150
151 </tests>
152 <help>
153
154 **What it does**
155
156 Allows one to find sequence variants and/or sites covered by a specified number of reads with bases above a set quality threshold. The tool works on six and ten column pileup formats produced with *samtools pileup* command. However, it also allows you to specify columns in the input file manually. The tool assumes the following:
157
158 - the quality scores follow phred33 convention, where input qualities are ASCII characters equal to the Phred quality plus 33.
159 - the pileup dataset was produced by the *samtools pileup* command (although you can override this by setting column assignments manually).
160
161 --------
162
163 **Types of pileup datasets**
164
165 The descriptions of the following pileup formats are largely based on information that can be found on the SAMTools_ documentation page. The 6- and 10-column variants are described below.
166
167 .. _SAMTools: http://samtools.sourceforge.net/pileup.shtml
168
169 **Six column pileup**::
170
171 1 2 3 4 5 6
172 ---------------------------------
173 chrM 412 A 2 ., II
174 chrM 413 G 4 ..t, IIIH
175 chrM 414 C 4 ..Ta III2
176 chrM 415 C 4 TTTt III7
177
178 where::
179
180 Column Definition
181 ------- ----------------------------
182 1 Chromosome
183 2 Position (1-based)
184 3 Reference base at that position
185 4 Coverage (# reads aligning over that position)
186 5 Bases within reads
187 6 Quality values (phred33 scale, see Galaxy wiki for more)
188
189 **Ten column pileup**
190
191 The `ten-column`__ pileup incorporates additional consensus information generated with the *-c* option of the *samtools pileup* command::
192
193
194 1 2 3 4 5 6 7 8 9 10
195 ------------------------------------------------
196 chrM 412 A A 75 0 25 2 ., II
197 chrM 413 G G 72 0 25 4 ..t, IIIH
198 chrM 414 C C 75 0 25 4 ..Ta III2
199 chrM 415 C T 75 75 25 4 TTTt III7
200
201 where::
202
203 Column Definition
204 ------- ----------------------------
205 1 Chromosome
206 2 Position (1-based)
207 3 Reference base at that position
208 4 Consensus bases
209 5 Consensus quality
210 6 SNP quality
211 7 Maximum mapping quality
212 8 Coverage (# reads aligning over that position)
213 9 Bases within reads
214 10 Quality values (phred33 scale, see Galaxy wiki for more)
215
216
217 .. __: http://samtools.sourceforge.net/cns0.shtml
218
219 ------
220
221 **The output format**
222
223 The tool modifies the input dataset in two ways:
224
225 1. It appends five columns to the end of every reported line:
226
227 - Number of **A** variants
228 - Number of **C** variants
229 - Number of **G** variants
230 - Number of **T** variants
231 - Number of read bases covering this position, where quality is equal to or higher than the value set by **Do not consider read bases with quality lower than** option.
232
233 Optionally, if **Print total number of differences?** is set to **Yes**, the tool will append the sixth column with the total number of deviants (see below).
234
235 2. If **Convert coordinates to intervals?** is set to **Yes**, the tool replaces the position column (typically the second column) with a pair of tab-delimited start/end values.
236
237 For example, if you are calling variants with base quality above 20 on this dataset::
238
239 chrM 412 A 2 ., II
240 chrM 413 G 4 ..t, III2
241 chrM 414 C 4 ..Ta III2
242 chrM 415 C 4 TTTt III7
243
244 you will get::
245
246 chrM 413 G 4 ..t, IIIH 0 0 2 1 3
247 chrM 414 C 4 ..Ta III2 1 1 0 1 3
248 chrM 415 C 4 TTTt III7 0 0 0 4 4
249
250 where::
251
252 Column Definition
253 ------- ----------------------------
254 1 Chromosome
255 2 Position (1-based)
256 3 Reference base at that position
257 4 Coverage (# reads aligning over that position)
258 5 Bases within reads where
259 6 Quality values (phred33 scale, see Galaxy wiki for more)
260 7 Number of A variants
261 8 Number of C variants
262 9 Number of G variants
263 10 Number of T variants
264 11 Quality adjusted coverage:
265 12 Number of read bases (i.e., # of reads) with quality above the set threshold
266 13 Total number of deviants (if Convert coordinates to intervals? is set to yes)
267
268 if **Print total number of differences?** is set to **Yes**, you will get::
269
270 chrM 413 G 4 ..t, IIIH 0 0 2 1 3 1
271 chrM 414 C 4 ..Ta III2 1 2 0 1 3 2
272 chrM 415 C 4 TTTt III7 0 0 0 4 4 0
273
274 Note the additional column 13, that contains the number of deviant reads (e.g., there are two deviants, T and a, for position 414).
275
276
277 Finally, if **Convert coordinates to intervals?** is set to **Yes**, you will get one additional column with the end coordinate::
278
279 chrM 412 413 G 4 ..t, III2 0 0 2 1 3
280 chrM 414 415 C 4 ..Ta III2 1 2 0 1 3
281 chrM 414 415 C 4 TTTt III7 0 0 0 4 4
282
283 where::
284
285 Column Definition
286 ------- ----------------------------
287 1 Chromosome
288 2 Start position (0-based)
289 3 End position (1-based)
290 4 Reference base at that position
291 5 Coverage (# reads aligning over that position)
292 6 Bases within reads
293 7 Quality values (phred33 scale, see Galaxy wiki for more)
294 8 Number of A variants
295 9 Number of C variants
296 10 Number of G variants
297 11 Number of T variants
298 12 Quality adjusted coverage
299 13 Total number of deviants (if Convert coordinates to intervals? is set to yes)
300
301
302 Note that in this case the coordinates of SNPs were converted to intervals, where the start coordinate is 0-based and the end coordinate in 1-based using the UCSC Table Browser convention.
303
304 Although three positions have variants in the original file (413, 414, and 415), only 413 and 415 are reported because the quality values associated with these two SNPs are above the threshold of 20. In the case of 414 the **a** allele has a quality value of 17 ( ord("2")-33 ), and is therefore not reported. Note that five columns have been added to each of the reported lines::
305
306 chrM 413 G 4 ..t, IIIH 0 0 2 1 3
307
308 Here, there is one variant, **t**. Because the fourth column represents **T** counts, it is incremented by 1. The last column shows that at this position, three reads have bases above the quality threshold of 20.
309
310 -----
311
312 **Example 1**: Just variants
313
314 In this mode, the tool only outputs the lines from the input datasets where at least one read contains a sequence variant with quality above the threshold set by the **Do not consider read bases with quality lower than** option. For example, suppose one has a pileup dataset like the following::
315
316 chrM 412 A 2 ., II
317 chrM 413 G 4 ..t, III2
318 chrM 414 C 4 ..Ta III2
319 chrM 415 C 4 TTTt III7
320
321 To call all variants (with no restriction by coverage) with quality above phred value of 20, we will need to set the parameters as follows:
322
323 .. image:: ./static/images/pileup_parser_help1.png
324
325 Running the tool with these parameters will return::
326
327 chrM 413 G 4 ..t, IIIH 0 0 0 1 3
328 chrM 414 C 4 ..Ta III2 0 2 0 1 3
329 chrM 415 C 4 TTTt III7 0 0 0 4 4
330
331 **Note** that position 414 is not reported because the *a* variant has associated quality value of 17 (because ord('2')-33 = 17) and is below the phred threshold of 20 set by the **Count variants with quality above this value** parameter.
332
333 -----
334
335 **Example 2**: Report everything
336
337 In addition to calling variants, it is often useful to know the quality adjusted coverage. Running the tool with these parameters:
338
339 .. image:: ./static/images/pileup_parser_help2.png
340
341 will report everything from the original file::
342
343 chrM 412 A 2 ., II 2 0 0 0 2
344 chrM 413 G 4 ..t, III2 0 0 2 1 3
345 chrM 414 C 4 ..Ta III2 0 2 0 1 3
346 chrM 415 C 4 TTTt III7 0 0 0 4 4
347
348 Here, you can see that although the total coverage at position 414 is 4 (column 4), the quality adjusted coverage is 3 (last column). This is because only three out of four reads have bases with quality above the set threshold of 20 (the actual qualities are III2 or, after conversion, 40, 40, 40, 17).
349
350 One can use the last column of this dataset to filter out (using Galaxy's **Filter** tool) positions where quality adjusted coverage (last column) is below a set threshold.
351
352 ------
353
354 **Example 3**: Report everything and print total number of differences
355
356 If you set the **Print total number of differences?** to **Yes** the tool will print an additional column with the total number of reads where a devinat base is above the quality threshold. So, seetiing parametrs like this:
357
358 .. image:: ./static/images/pileup_parser_help3.png
359
360 will produce this::
361
362 chrM 412 A 2 ., II 2 0 0 0 2 0
363 chrM 413 G 4 ..t, III2 0 0 2 1 3 1
364 chrM 414 C 4 ..Ta III2 0 2 0 1 3 1
365 chrM 415 C 4 TTTt III7 0 0 0 4 4 0
366
367
368 -----
369
370 **Example 4**: Report everything, print total number of differences, and ignore qualities and read bases
371
372 Setting **Print quality and base string?** to **Yes** as shown here:
373
374 .. image:: ./static/images/pileup_parser_help4.png
375
376 will produce this::
377
378 chrM 412 A 2 2 0 0 0 2 0
379 chrM 413 G 4 0 0 2 1 3 1
380 chrM 414 C 4 0 2 0 1 3 1
381 chrM 415 C 4 0 0 0 4 4 0
382
383
384
385
386 </help>
387 </tool>