annotate snpSift_filter.xml @ 6:2b3e65a4252f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 693e1a3641c776965f68d688c8e1409adba7da1e
author iuc
date Wed, 16 Jan 2019 15:35:26 -0500
parents 09d6806c609e
children 2e497a770bca
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
09d6806c609e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 70ff70918368ff0deeb596c2190a770abe9e1c9b
iuc
parents: 3
diff changeset
1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.galaxy0">
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 <command><![CDATA[
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
10 SnpSift -Xmx6G filter -f '$input' -e '$exprFile' $inverse
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
11 #if $filtering.mode == 'field':
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
12 #if $filtering.replace.pass:
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
13 --pass
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
14 #if $filtering.replace.filterId.strip():
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
15 --filterId '$filtering.replace.filterId'
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
16 #end if
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
17 #end if
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
18 #if $filtering.addFilter.strip():
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
19 --addFilter '$filtering.addFilter'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
20 #end if
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
21 #if $filtering.rmFilter.strip():
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
22 --rmFilter '$filtering.rmFilter'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
23 #end if
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
24 #end if
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
25 > '$output'
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
26 ]]></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
27 <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
28 <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
29 $expr#slurp
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
30 </configfile>
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
31 </configfiles>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
32 <inputs>
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
33 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
34 <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples">
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
35 <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
36 </param>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
37 <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
38 <conditional name="filtering">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
39 <param name="mode" type="select" label="Filter mode">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
40 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
41 <option value="field">Change the FILTER field, but retain all entries</option>
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
42 </param>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
43 <when value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
44 <when value="field">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
45 <conditional name="replace">
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
46 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
47 help="appends an ID tag to non-matching entry FILTER" />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
48 <when value="no"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
49 <when value="yes">
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
50 <param name="filterId" type="text" value="" label="ID appended to non-matching (##FILTER tag in header and FILTER VCF field)" help="Default ID is 'SnpSift'"/>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
51 </when>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
52 </conditional>
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
53 <param name="addFilter" type="text" value="" label="Add a string to FILTER VCF field if 'expression' is true" />
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
54 <param name="rmFilter" type="text" value="" 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
55 </when>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
56 </conditional>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
57 </inputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
58
9e8280e19338 Uploaded
iuc
parents:
diff changeset
59 <outputs>
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
60 <data name="output" format="vcf" />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
61 </outputs>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
62 <tests>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
63 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
64 <param name="input" ftype="vcf" value="test01.vcf"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
65 <param name="expr" value="QUAL >= 50"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
66 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
67 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
68 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
69 <has_text text="28837706" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
70 <not_has_text text="NT_166464" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
71 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
72 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
73 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
74
9e8280e19338 Uploaded
iuc
parents:
diff changeset
75 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
76 <param name="input" ftype="vcf" value="test01.vcf"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
77 <param name="expr" value="(CHROM = '19')"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
78 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
79 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
80 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
81 <has_text text="3205820" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
82 <not_has_text text="NT_16" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
83 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
84 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
85 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
86
9e8280e19338 Uploaded
iuc
parents:
diff changeset
87 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
88 <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
89 <param name="expr" value="(POS &gt;= 20175) &amp; (POS &lt;= 35549)"/>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
90 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
91 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
92 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
93 <has_text text="20175" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
94 <has_text text="35549" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
95 <has_text text="22256" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
96 <not_has_text text="18933" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
97 <not_has_text text="37567" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
98 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
99 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
100 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
101
9e8280e19338 Uploaded
iuc
parents:
diff changeset
102 <test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
103 <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
104 <param name="expr" value="( DP &gt;= 5 )"/>
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
105 <param name="mode" value="entries"/>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
106 <output name="output">
9e8280e19338 Uploaded
iuc
parents:
diff changeset
107 <assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
108 <has_text text="DP=5;" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
109 <has_text text="DP=6;" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
110 <not_has_text text="DP=1;" />
9e8280e19338 Uploaded
iuc
parents:
diff changeset
111 </assert_contents>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
112 </output>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
113 </test>
9e8280e19338 Uploaded
iuc
parents:
diff changeset
114 </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
115 <help><![CDATA[
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
116 **SnpSift filter**
9e8280e19338 Uploaded
iuc
parents:
diff changeset
117
9e8280e19338 Uploaded
iuc
parents:
diff changeset
118 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
119
9e8280e19338 Uploaded
iuc
parents:
diff changeset
120 Some examples:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
121
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
122 - *I want just the variants from the second million bases of chr1*::
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
123
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
124 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
125
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
126 - *Filter value is either 'PASS' or it is missing*::
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
127
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
128 (FILTER = 'PASS') | ( na FILTER )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
129
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
130 - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*::
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
131
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
132 ( ANN[*].EFFECT has 'frameshift_variant' )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
133
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
134 **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.
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
135
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
136 - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*::
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
137
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
138 ( EFF[*].EFFECT = 'FRAME_SHIFT' )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
139
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
140 - *I want to filter out samples with quality less than 30*::
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
141
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
142 ( QUAL > 30 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
143
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
144 - *...but we also want InDels that have quality 20 or more*::
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
145
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
146 (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
147
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
148 - *...or any homozygous variant present in more than 3 samples*::
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
149
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
150 (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
151
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
152 - *...or any heterozygous sample with coverage 25 or more*::
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
153
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
154 ((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 )
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
155
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
156 - *I want to keep samples where the genotype for the first sample is homozygous variant and the genotype for the second sample is reference*::
2
bf8c1526871b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
parents: 1
diff changeset
157
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
158 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
159
9e8280e19338 Uploaded
iuc
parents:
diff changeset
160 **For information regarding HGVS and Sequence Ontology terms versus classic names**:
9e8280e19338 Uploaded
iuc
parents:
diff changeset
161
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
162 - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
163 - http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
164
9e8280e19338 Uploaded
iuc
parents:
diff changeset
165 @EXTERNAL_DOCUMENTATION@
3
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
166 - http://snpeff.sourceforge.net/SnpSift.html#filter
20c7d583fec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
parents: 2
diff changeset
167 ]]></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
168 <expand macro="citations" />
0
9e8280e19338 Uploaded
iuc
parents:
diff changeset
169 </tool>