Mercurial > repos > iuc > snpsift
annotate snpSift_filter.xml @ 3:20c7d583fec1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
author | iuc |
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date | Mon, 12 Jun 2017 10:25:32 -0400 |
parents | bf8c1526871b |
children | 09d6806c609e |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0"> |
0 | 2 <description>Filter variants using arbitrary expressions</description> |
3 <macros> | |
4 <import>snpSift_macros.xml</import> | |
5 </macros> | |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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6 <expand macro="requirements" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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7 <expand macro="stdio" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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8 <expand macro="version_command" /> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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9 <command><![CDATA[ |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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
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11 #if $filtering.mode == 'field': |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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12 #if $filtering.replace.pass: |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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13 --pass |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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14 #if $filtering.replace.filterId.strip(): |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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15 --filterId '$filtering.replace.filterId' |
0 | 16 #end if |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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17 #end if |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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18 #if $filtering.addFilter.strip(): |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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19 --addFilter '$filtering.addFilter' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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20 #end if |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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21 #if $filtering.rmFilter.strip(): |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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22 --rmFilter '$filtering.rmFilter' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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23 #end if |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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24 #end if |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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25 > '$output' |
20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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26 ]]></command> |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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27 <configfiles> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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28 <configfile name="exprFile"> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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29 $expr#slurp |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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30 </configfile> |
1
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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31 </configfiles> |
0 | 32 <inputs> |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
iuc
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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
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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
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35 <sanitizer sanitize="False"/> |
98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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36 </param> |
0 | 37 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" /> |
38 <conditional name="filtering"> | |
39 <param name="mode" type="select" label="Filter mode"> | |
40 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option> | |
41 <option value="field">Change the FILTER field, but retain all entries</option> | |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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42 </param> |
0 | 43 <when value="entries"/> |
44 <when value="field"> | |
45 <conditional name="replace"> | |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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46 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'" |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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47 help="appends an ID tag to non-matching entry FILTER" /> |
0 | 48 <when value="no"/> |
49 <when value="yes"> | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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 | 51 </when> |
52 </conditional> | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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
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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 | 55 </when> |
56 </conditional> | |
57 </inputs> | |
58 | |
59 <outputs> | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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60 <data name="output" format="vcf" /> |
0 | 61 </outputs> |
62 <tests> | |
63 <test> | |
64 <param name="input" ftype="vcf" value="test01.vcf"/> | |
65 <param name="expr" value="QUAL >= 50"/> | |
66 <param name="mode" value="entries"/> | |
67 <output name="output"> | |
68 <assert_contents> | |
69 <has_text text="28837706" /> | |
70 <not_has_text text="NT_166464" /> | |
71 </assert_contents> | |
72 </output> | |
73 </test> | |
74 | |
75 <test> | |
76 <param name="input" ftype="vcf" value="test01.vcf"/> | |
77 <param name="expr" value="(CHROM = '19')"/> | |
78 <param name="mode" value="entries"/> | |
79 <output name="output"> | |
80 <assert_contents> | |
81 <has_text text="3205820" /> | |
82 <not_has_text text="NT_16" /> | |
83 </assert_contents> | |
84 </output> | |
85 </test> | |
86 | |
87 <test> | |
88 <param name="input" ftype="vcf" value="test01.vcf"/> | |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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89 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/> |
0 | 90 <param name="mode" value="entries"/> |
91 <output name="output"> | |
92 <assert_contents> | |
93 <has_text text="20175" /> | |
94 <has_text text="35549" /> | |
95 <has_text text="22256" /> | |
96 <not_has_text text="18933" /> | |
97 <not_has_text text="37567" /> | |
98 </assert_contents> | |
99 </output> | |
100 </test> | |
101 | |
102 <test> | |
103 <param name="input" ftype="vcf" value="test01.vcf"/> | |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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104 <param name="expr" value="( DP >= 5 )"/> |
0 | 105 <param name="mode" value="entries"/> |
106 <output name="output"> | |
107 <assert_contents> | |
108 <has_text text="DP=5;" /> | |
109 <has_text text="DP=6;" /> | |
110 <not_has_text text="DP=1;" /> | |
111 </assert_contents> | |
112 </output> | |
113 </test> | |
114 </tests> | |
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98708b88af9f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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115 <help><![CDATA[ |
0 | 116 **SnpSift filter** |
117 | |
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. | |
119 | |
120 Some examples: | |
121 | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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122 - *I want just the variants from the second million bases of chr1*:: |
0 | 123 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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124 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 ) |
0 | 125 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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126 - *Filter value is either 'PASS' or it is missing*:: |
0 | 127 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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128 (FILTER = 'PASS') | ( na FILTER ) |
0 | 129 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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130 - *I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )*:: |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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131 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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132 ( ANN[*].EFFECT has 'frameshift_variant' ) |
0 | 133 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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135 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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136 - *I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )*:: |
0 | 137 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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138 ( EFF[*].EFFECT = 'FRAME_SHIFT' ) |
0 | 139 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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140 - *I want to filter out samples with quality less than 30*:: |
0 | 141 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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142 ( QUAL > 30 ) |
0 | 143 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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144 - *...but we also want InDels that have quality 20 or more*:: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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145 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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146 (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 ) |
0 | 147 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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148 - *...or any homozygous variant present in more than 3 samples*:: |
0 | 149 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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150 (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 ) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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151 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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152 - *...or any heterozygous sample with coverage 25 or more*:: |
0 | 153 |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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154 ((countHet() > 0) & (DP >= 25)) | (countHom() > 3) | (( exists INDEL ) & (QUAL >= 20)) | (QUAL >= 30 ) |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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*:: |
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bf8c1526871b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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157 |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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158 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] )) |
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160 **For information regarding HGVS and Sequence Ontology terms versus classic names**: | |
161 | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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
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163 - http://snpeff.sourceforge.net/SnpEff_manual.html#input for the table containing the classic name and sequence onology term for each effect |
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165 @EXTERNAL_DOCUMENTATION@ | |
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20c7d583fec1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5
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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
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167 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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168 <expand macro="citations" /> |
0 | 169 </tool> |