annotate snpSift_filter.xml @ 1:98708b88af9f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
author iuc
date Tue, 07 Jun 2016 10:04:09 -0400
parents 9e8280e19338
children bf8c1526871b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
2 <description>Filter variants using arbitrary expressions</description>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
3 <macros>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
4 <import>snpSift_macros.xml</import>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
5 </macros>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
6 <expand macro="requirements" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
7 <expand macro="stdio" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
8 <expand macro="version_command" />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
9
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
10 <command><![CDATA[
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
11 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
12 #if $filtering.mode == 'field':
9e8280e19338 Uploaded
iuc
parents:
diff changeset
13 #if $filtering.replace.pass:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
14 --pass
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
15 #if $filtering.replace.filterId and len(str($filtering.replace.filterId).strip()) > 0:
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
16 --filterId "$filtering.replace.filterId"
9e8280e19338 Uploaded
iuc
parents:
diff changeset
17 #end if
9e8280e19338 Uploaded
iuc
parents:
diff changeset
18 #end if
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
19 #if $filtering.addFilter and len(str($filtering.addFilter).strip()) > 0:
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
20 --addFilter "$filtering.addFilter"
9e8280e19338 Uploaded
iuc
parents:
diff changeset
21 #end if
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
22 #if $filtering.rmFilter and len(str($filtering.rmFilter).strip()) > 0:
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
23 --rmFilter "$filtering.rmFilter"
9e8280e19338 Uploaded
iuc
parents:
diff changeset
24 #end if
9e8280e19338 Uploaded
iuc
parents:
diff changeset
25 #end if
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
26 > "$output"
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
27 ]]>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
28 </command>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
29 <configfiles>
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
30 <configfile name="exprFile">
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
31 $expr#slurp
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
32 </configfile>
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
33 </configfiles>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
34 <inputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
35 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
36 <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." >
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
37 <sanitizer sanitize="False"/>
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
38 </param>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
39 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
40 <conditional name="filtering">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
41 <param name="mode" type="select" label="Filter mode">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
42 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
43 <option value="field">Change the FILTER field, but retain all entries</option>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
44 </param>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
45 <when value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
46 <when value="field">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
47 <conditional name="replace">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
48 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
9e8280e19338 Uploaded
iuc
parents:
diff changeset
49 help="appends an ID tag to non-matching entry FILTER "/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
50 <when value="no"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
51 <when value="yes">
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
52 <param name="filterId" type="text" value="" optional="true" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)."
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
53 help="Default ID is 'SnpSift'"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
54 </when>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
55 </conditional>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
56 <param name="addFilter" type="text" value="" optional="true" label="Add a string to FILTER VCF field if 'expression' is true." />
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
57 <param name="rmFilter" type="text" value="" optional="true" label="Remove a string from FILTER VCF field if 'expression' is true (and 'str' is in the field)." />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
58 </when>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
59 </conditional>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
60 </inputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
61
9e8280e19338 Uploaded
iuc
parents:
diff changeset
62 <outputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
63 <data format="vcf" name="output" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
64 </outputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
65 <tests>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
66 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
67 <param name="input" ftype="vcf" value="test01.vcf"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
68 <param name="expr" value="QUAL >= 50"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
69 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
70 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
71 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
72 <has_text text="28837706" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
73 <not_has_text text="NT_166464" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
74 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
75 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
76 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
77
9e8280e19338 Uploaded
iuc
parents:
diff changeset
78 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
79 <param name="input" ftype="vcf" value="test01.vcf"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
80 <param name="expr" value="(CHROM = '19')"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
81 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
82 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
83 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
84 <has_text text="3205820" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
85 <not_has_text text="NT_16" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
86 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
87 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
88 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
89
9e8280e19338 Uploaded
iuc
parents:
diff changeset
90 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
91 <param name="input" ftype="vcf" value="test01.vcf"/>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
92 <param name="expr" value="(POS &gt;= 20175) &amp; (POS &lt;= 35549)"/>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
93 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
94 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
95 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
96 <has_text text="20175" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
97 <has_text text="35549" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
98 <has_text text="22256" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
99 <not_has_text text="18933" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
100 <not_has_text text="37567" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
101 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
102 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
103 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
104
9e8280e19338 Uploaded
iuc
parents:
diff changeset
105 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
106 <param name="input" ftype="vcf" value="test01.vcf"/>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
107 <param name="expr" value="( DP &gt;= 5 )"/>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
108 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
109 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
110 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
111 <has_text text="DP=5;" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
112 <has_text text="DP=6;" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
113 <not_has_text text="DP=1;" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
114 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
115 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
116 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
117 </tests>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
118 <help><![CDATA[
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
119
9e8280e19338 Uploaded
iuc
parents:
diff changeset
120 **SnpSift filter**
9e8280e19338 Uploaded
iuc
parents:
diff changeset
121
9e8280e19338 Uploaded
iuc
parents:
diff changeset
122 You can filter a VCF file using arbitrary expressions, for instance "(QUAL > 30) | (exists INDEL) | ( countHet() > 2 )". The actual expressions can be quite complex, so it allows for a lot of flexibility.
9e8280e19338 Uploaded
iuc
parents:
diff changeset
123
9e8280e19338 Uploaded
iuc
parents:
diff changeset
124 Some examples:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
125
9e8280e19338 Uploaded
iuc
parents:
diff changeset
126 - *I want just the variants from the second million bases of chr1*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
127
9e8280e19338 Uploaded
iuc
parents:
diff changeset
128 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
129
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
130 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
131
9e8280e19338 Uploaded
iuc
parents:
diff changeset
132 - *Filter value is either 'PASS' or it is missing*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
133
9e8280e19338 Uploaded
iuc
parents:
diff changeset
134 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
135
9e8280e19338 Uploaded
iuc
parents:
diff changeset
136 (FILTER = 'PASS') | ( na FILTER )
9e8280e19338 Uploaded
iuc
parents:
diff changeset
137
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
138 - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
139
9e8280e19338 Uploaded
iuc
parents:
diff changeset
140 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
141
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
142 ( ANN[*].EFFECT has 'frameshift_variant' )
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
143
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
144 **Important** According to the specification, there can be more than one EFFECT separated by & (e.g. 'missense_variant&splice_region_variant', thus using has operator is better than using equality operator (=). For instance 'missense_variant&splice_region_variant' = 'missense_variant' is false, whereas 'missense_variant&splice_region_variant' has 'missense_variant' is true.
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
145
9e8280e19338 Uploaded
iuc
parents:
diff changeset
146 - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
147
9e8280e19338 Uploaded
iuc
parents:
diff changeset
148 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
149
9e8280e19338 Uploaded
iuc
parents:
diff changeset
150 ( EFF[*].EFFECT = 'FRAME_SHIFT' )
9e8280e19338 Uploaded
iuc
parents:
diff changeset
151
9e8280e19338 Uploaded
iuc
parents:
diff changeset
152 - *I want to filter out samples with quality less than 30*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
153
9e8280e19338 Uploaded
iuc
parents:
diff changeset
154 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
155
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
156 ( QUAL > 30 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
157
9e8280e19338 Uploaded
iuc
parents:
diff changeset
158 - *...but we also want InDels that have quality 20 or more*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
159
9e8280e19338 Uploaded
iuc
parents:
diff changeset
160 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
161
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
162 (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
163
9e8280e19338 Uploaded
iuc
parents:
diff changeset
164 - *...or any homozygous variant present in more than 3 samples*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
165
9e8280e19338 Uploaded
iuc
parents:
diff changeset
166 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
167
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
168 (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
169
9e8280e19338 Uploaded
iuc
parents:
diff changeset
170 - *...or any heterozygous sample with coverage 25 or more*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
171
9e8280e19338 Uploaded
iuc
parents:
diff changeset
172 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
173
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
174 ((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
175
9e8280e19338 Uploaded
iuc
parents:
diff changeset
176 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
177
9e8280e19338 Uploaded
iuc
parents:
diff changeset
178 ::
9e8280e19338 Uploaded
iuc
parents:
diff changeset
179
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
180 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
181
9e8280e19338 Uploaded
iuc
parents:
diff changeset
182
9e8280e19338 Uploaded
iuc
parents:
diff changeset
183 **For information regarding HGVS and Sequence Ontology terms versus classic names**:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
184
9e8280e19338 Uploaded
iuc
parents:
diff changeset
185 - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
9e8280e19338 Uploaded
iuc
parents:
diff changeset
186 - http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect
9e8280e19338 Uploaded
iuc
parents:
diff changeset
187
9e8280e19338 Uploaded
iuc
parents:
diff changeset
188
9e8280e19338 Uploaded
iuc
parents:
diff changeset
189 @EXTERNAL_DOCUMENTATION@
9e8280e19338 Uploaded
iuc
parents:
diff changeset
190 http://snpeff.sourceforge.net/SnpSift.html#filter
9e8280e19338 Uploaded
iuc
parents:
diff changeset
191
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
192 ]]>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
193 </help>
1
98708b88af9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
parents: 0
diff changeset
194 <expand macro="citations" />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
195 </tool>