snpsift: snpSift_filter.xml annotate

annotate snpSift_filter.xml @ 15:8bd645802765 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5

author	iuc
date	Mon, 12 Jun 2017 10:24:36 -0400
parents	80da7fae14b8
children	ede8954f5c82

rev	line source
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	1 <tool id="snpSift_filter" name="SnpSift Filter" version="@WRAPPER_VERSION@.0">
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 <command><![CDATA[
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	10 SnpSift -Xmx6G filter -f '$input' -e '$exprFile' $inverse
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	11 #if $filtering.mode == 'field':
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	12 #if $filtering.replace.pass:
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	13 --pass
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	14 #if $filtering.replace.filterId.strip():
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	15 --filterId '$filtering.replace.filterId'
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	16 #end if
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	17 #end if
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	18 #if $filtering.addFilter.strip():
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	19 --addFilter '$filtering.addFilter'
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	20 #end if
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	21 #if $filtering.rmFilter.strip():
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	22 --rmFilter '$filtering.rmFilter'
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	23 #end if
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	24 #end if
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	25 > '$output'
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	26 ]]></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	27 <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	28 <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	29 $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	30 </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	31 </configfiles>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	32 <inputs>
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	33 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	34 <param name="expr" type="text" label="Filter criteria" help="Need help? See below a few examples">
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	35 <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	36 </param>
0 f0faaa4d6ee5 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" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	38 <conditional name="filtering">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	39 <param name="mode" type="select" label="Filter mode">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	40 <option value="entries" selected="true">Retain entries that pass filter, remove other entries</option>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	41 <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	42 </param>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	43 <when value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	44 <when value="field">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	45 <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	46 <param name="pass" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Set matching entry FILTER to 'PASS'"
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	47 help="appends an ID tag to non-matching entry FILTER" />
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	48 <when value="no"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	49 <when value="yes">
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 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 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	51 </when>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	52 </conditional>
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	53 <param name="addFilter" type="text" value="" label="Add a string to FILTER VCF field if 'expression' is true" />
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 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 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	55 </when>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	56 </conditional>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	57 </inputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	58
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	59 <outputs>
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	60 <data name="output" format="vcf" />
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	61 </outputs>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	62 <tests>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	63 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	64 <param name="input" ftype="vcf" value="test01.vcf"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	65 <param name="expr" value="QUAL >= 50"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	66 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	67 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	68 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	69 <has_text text="28837706" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	70 <not_has_text text="NT_166464" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	71 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	72 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	73 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	74
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	75 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	76 <param name="input" ftype="vcf" value="test01.vcf"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	77 <param name="expr" value="(CHROM = '19')"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	78 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	79 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	80 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	81 <has_text text="3205820" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	82 <not_has_text text="NT_16" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	83 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	84 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	85 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	86
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	87 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	88 <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	89 <param name="expr" value="(POS >= 20175) & (POS <= 35549)"/>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	90 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	91 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	92 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	93 <has_text text="20175" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	94 <has_text text="35549" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	95 <has_text text="22256" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	96 <not_has_text text="18933" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	97 <not_has_text text="37567" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	98 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	99 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	100 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	101
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	102 <test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	103 <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	104 <param name="expr" value="( DP >= 5 )"/>
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	105 <param name="mode" value="entries"/>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	106 <output name="output">
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	107 <assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	108 <has_text text="DP=5;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	109 <has_text text="DP=6;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	110 <not_has_text text="DP=1;" />
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	111 </assert_contents>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	112 </output>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	113 </test>
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	114 </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	115 <help><![CDATA[
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	116 SnpSift filter
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	117
f0faaa4d6ee5 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.
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	119
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	120 Some examples:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	121
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	122 - I want just the variants from the second million bases of chr1::
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	123
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	124 ( CHROM = 'chr1' ) & ( POS > 1000000 ) & ( POS < 2000000 )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	125
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	126 - Filter value is either 'PASS' or it is missing::
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	127
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	128 (FILTER = 'PASS') \| ( na FILTER )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	129
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	130 - I want to filter lines with an ANN annotation EFFECT of 'frameshift_variant' ( for vcf files using Sequence Ontology terms )::
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	131
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	132 ( ANN[*].EFFECT has 'frameshift_variant' )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	133
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 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.
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	135
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	136 - I want to filter lines with an EFF of 'FRAME_SHIFT' ( for vcf files using Classic Effect names )::
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	137
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	138 ( EFF[*].EFFECT = 'FRAME_SHIFT' )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	139
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	140 - I want to filter out samples with quality less than 30::
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	141
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	142 ( QUAL > 30 )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	143
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	144 - ...but we also want InDels that have quality 20 or more::
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	145
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	146 (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	147
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	148 - ...or any homozygous variant present in more than 3 samples::
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	149
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	150 (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	151
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	152 - ...or any heterozygous sample with coverage 25 or more::
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	153
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	154 ((countHet() > 0) & (DP >= 25)) \| (countHom() > 3) \| (( exists INDEL ) & (QUAL >= 20)) \| (QUAL >= 30 )
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	155
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 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::
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	157
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	158 (isHom( GEN[0] ) & isVariant( GEN[0] ) & isRef( GEN[1] ))
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	159
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	160 For information regarding HGVS and Sequence Ontology terms versus classic names:
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	161
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	162 - http://snpeff.sourceforge.net/SnpEff_manual.html#cmdline for the options: -classic, -hgvs, and -sequenceOntology
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 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 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	164
f0faaa4d6ee5 Uploaded iuc parents: diff changeset	165 @EXTERNAL_DOCUMENTATION@
15 8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	166 - http://snpeff.sourceforge.net/SnpSift.html#filter
8bd645802765 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 14 diff changeset	167 ]]></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	168 <expand macro="citations" />
0 f0faaa4d6ee5 Uploaded iuc parents: diff changeset	169 </tool>

Mercurial > repos > iuc > snpsift

annotate snpSift_filter.xml @ 15:8bd645802765 draft