snpsift: snpSift_filter.xml annotate

annotate snpSift_filter.xml @ 14:80da7fae14b8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f

author	iuc
date	Mon, 05 Dec 2016 12:10:54 -0500
parents	ed810da439cc
children	8bd645802765

rev	line source
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.1">
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	2 <description>Filter variants using arbitrary expressions</description>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	3 <macros>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	4 <import>snpSift_macros.xml</import>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	5 </macros>
11 b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	6 <expand macro="requirements" />
b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	7 <expand macro="stdio" />
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	8 <expand macro="version_command" />
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	9
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	10 <command><![CDATA[
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	11 @CONDA_SNPSIFT_JAR_PATH@ &&
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	12 java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" filter -f "$input" -e "$exprFile" $inverse
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	13 #if $filtering.mode == 'field':
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	14 #if $filtering.replace.pass:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	15 --pass
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	16 #if $filtering.replace.filterId and len(str($filtering.replace.filterId).strip()) > 0:
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	17 --filterId "$filtering.replace.filterId"
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	18 #end if
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	19 #end if
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	20 #if $filtering.addFilter and len(str($filtering.addFilter).strip()) > 0:
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	21 --addFilter "$filtering.addFilter"
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	22 #end if
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	23 #if $filtering.rmFilter and len(str($filtering.rmFilter).strip()) > 0:
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	24 --rmFilter "$filtering.rmFilter"
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	25 #end if
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	26 #end if
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	27 > "$output"
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	28 ]]>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	29 </command>
11 b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	30 <configfiles>
b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	31 <configfile name="exprFile">
b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	32 $expr#slurp
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	33 </configfile>
11 b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	34 </configfiles>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	35 <inputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	36 <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	37 <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples." >
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	38 <sanitizer sanitize="False"/>
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	39 </param>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	40 <param name="inverse" type="boolean" truevalue="--inverse" falsevalue="" checked="false" label="Inverse filter" help="Show lines that do not match filter expression" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	41 <conditional name="filtering">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	42 <param name="mode" type="select" label="Filter mode">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	43 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	44 <option value="field">Change the FILTER field, but retain all entries</option>
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	45 </param>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	46 <when value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	47 <when value="field">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	48 <conditional name="replace">
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	49 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	50 help="appends an ID tag to non-matching entry FILTER "/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	51 <when value="no"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	52 <when value="yes">
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	53 <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 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	54 </when>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	55 </conditional>
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	56 <param name="addFilter" type="text" value="" label="Add a string to FILTER VCF field if 'expression' is true." />
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	57 <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 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	58 </when>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	59 </conditional>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	60 </inputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	61
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	62 <outputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	63 <data format="vcf" name="output" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	64 </outputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	65 <tests>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	66 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	67 <param name="input" ftype="vcf" value="test01.vcf"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	68 <param name="expr" value="QUAL >= 50"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	69 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	70 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	71 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	72 <has_text text="28837706" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	73 <not_has_text text="NT_166464" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	74 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	75 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	76 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	77
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	78 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	79 <param name="input" ftype="vcf" value="test01.vcf"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	80 <param name="expr" value="(CHROM = '19')"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	81 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	82 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	83 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	84 <has_text text="3205820" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	85 <not_has_text text="NT_16" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	86 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	87 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	88 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	89
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	90 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	91 <param name="input" ftype="vcf" value="test01.vcf"/>
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	92 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	93 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	94 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	95 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	96 <has_text text="20175" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	97 <has_text text="35549" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	98 <has_text text="22256" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	99 <not_has_text text="18933" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	100 <not_has_text text="37567" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	101 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	102 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	103 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	104
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	105 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	106 <param name="input" ftype="vcf" value="test01.vcf"/>
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	107 <param name="expr" value="( DP >= 5 )"/>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	108 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	109 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	110 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	111 <has_text text="DP=5;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	112 <has_text text="DP=6;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	113 <not_has_text text="DP=1;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	114 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	115 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	116 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	117 </tests>
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	118 <help><![CDATA[
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	119
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	120 SnpSift filter
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	121
f0faaa4d6ee5 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.
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	123
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	124 Some examples:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	125
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	126 - I want just the variants from the second million bases of chr1:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	127
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	128 ::
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	129
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	130 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	131
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	132 - Filter value is either 'PASS' or it is missing:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	133
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	134 ::
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	135
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	136 (FILTER = 'PASS') \| ( na FILTER )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	137
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	138 - I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms ):
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	139
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	140 ::
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	141
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	142 ( ANN[*].EFFECT has 'frameshift_variant' )
11 b884686a80dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 344140b8df53b8b7024618bb04594607a045c03a iuc parents: 0 diff changeset	143
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 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 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	145
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	146 - I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names ):
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	147
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	148 ::
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	149
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	150 ( EFF[*].EFFECT = 'FRAME_SHIFT' )
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	151
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	152 - I want to filter out samples with quality less than 30:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	153
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	154 ::
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	155
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	156 ( QUAL > 30 )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	157
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	158 - ...but we also want InDels that have quality 20 or more:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	159
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	160 ::
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	161
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	162 (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	163
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	164 - ...or any homozygous variant present in more than 3 samples:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	165
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	166 ::
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	167
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	168 (countHom() > 3) \| (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	169
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	170 - ...or any heterozygous sample with coverage 25 or more:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	171
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	172 ::
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	173
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	174 ((countHet() > 0) & (DP >= 25)) \| (countHom() > 3) \| (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	175
0 f0faaa4d6ee5 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:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	177
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	178 ::
14 80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 13 diff changeset	179
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	180 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	181
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	182
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	183 For information regarding HGVS and Sequence Ontology terms versus classic names:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	184
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	185 - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
f0faaa4d6ee5 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
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	187
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	188
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	189 @EXTERNAL_DOCUMENTATION@
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	190 http://snpeff.sourceforge.net/SnpSift.html#filter
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	191
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	192 ]]>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	193 </help>
13 ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e iuc parents: 12 diff changeset	194 <expand macro="citations" />
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	195 </tool>

Mercurial > repos > iuc > snpsift

annotate snpSift_filter.xml @ 14:80da7fae14b8 draft