snpsift_dbnsfp: snpSift_dbnsfp.xml annotate

annotate snpSift_dbnsfp.xml @ 4:4e21e4f2bc48 draft default tip

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

author	iuc
date	Mon, 12 Jun 2017 10:25:44 -0400
parents	c838e7136a40
children

rev	line source
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0">
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	2 <description>Add annotations from dbNSFP or similar annotation DBs</description>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	3 <macros>
dc480609d9c1 Uploaded iuc parents: diff changeset	4 <import>snpSift_macros.xml</import>
dc480609d9c1 Uploaded iuc parents: diff changeset	5 </macros>
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	6 <expand macro="requirements" />
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	7 <expand macro="stdio" />
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	8 <expand macro="version_command" />
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	9 <command><![CDATA[
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	10 SnpSift -Xmx6G dbnsfp -v
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	11 #if $db.dbsrc == 'cached':
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	12 -db '$db.dbnsfp'
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	13 #if $db.annotations and str($db.annotations) != '':
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	14 -f '$db.annotations'
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	15 #end if
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	16 #else:
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	17 -db '${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}'
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	18 #if $db.annotations and str($db.annotations) != '':
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	19 -f '$db.annotations'
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	20 #end if
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	21 #end if
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	22 '$input' > '$output'
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	23 2> tmp.err && grep -v file tmp.err
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	24 ]]></command>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	25 <inputs>
dc480609d9c1 Uploaded iuc parents: diff changeset	26 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
dc480609d9c1 Uploaded iuc parents: diff changeset	27 <conditional name="db">
dc480609d9c1 Uploaded iuc parents: diff changeset	28 <param name="dbsrc" type="select" label="dbNSFP ">
dc480609d9c1 Uploaded iuc parents: diff changeset	29 <option value="cached">Locally installed dbNSFP database </option>
dc480609d9c1 Uploaded iuc parents: diff changeset	30 <option value="history">dbNSFP database from your history</option>
dc480609d9c1 Uploaded iuc parents: diff changeset	31 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	32 <when value="cached">
dc480609d9c1 Uploaded iuc parents: diff changeset	33 <param name="dbnsfp" type="select" label="Genome">
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	34 <options from_data_table="snpsift_dbnsfps">
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	35 <column name="name" index="2"/>
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	36 <column name="value" index="3"/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	37 </options>
dc480609d9c1 Uploaded iuc parents: diff changeset	38 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	39 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	40 <options from_data_table="snpsift_dbnsfps">
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	41 <column name="name" index="4"/>
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	42 <column name="value" index="4"/>
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	43 <filter type="param_value" ref="dbnsfp" column="3" />
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	44 <filter type="multiple_splitter" column="4" separator=","/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	45 </options>
dc480609d9c1 Uploaded iuc parents: diff changeset	46 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	47 </when>
dc480609d9c1 Uploaded iuc parents: diff changeset	48 <when value="history">
dc480609d9c1 Uploaded iuc parents: diff changeset	49 <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>
dc480609d9c1 Uploaded iuc parents: diff changeset	50 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	51 <options>
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	52 <filter type="data_meta" ref="dbnsfpdb" key="annotation" />
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	53 </options>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	54 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	55 </when>
dc480609d9c1 Uploaded iuc parents: diff changeset	56 </conditional>
dc480609d9c1 Uploaded iuc parents: diff changeset	57 </inputs>
dc480609d9c1 Uploaded iuc parents: diff changeset	58 <outputs>
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	59 <data name="output" format="vcf" />
0 dc480609d9c1 Uploaded iuc parents: diff changeset	60 </outputs>
dc480609d9c1 Uploaded iuc parents: diff changeset	61 <tests>
2 c838e7136a40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 1 diff changeset	62 <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular
c838e7136a40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 1 diff changeset	63 is converted from dbnsfp.tabular to snpsiftdbnsfp format on-the-fly
c838e7136a40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 1 diff changeset	64 when this tool is run and annotation metadata is not available
c838e7136a40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 1 diff changeset	65 until after the conversion is completed.
0 dc480609d9c1 Uploaded iuc parents: diff changeset	66 <test>
2 c838e7136a40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 1 diff changeset	67 <param name="input" ftype="vcf" value="test_annotate_in.vcf"/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	68 <param name="dbsrc" value="history"/>
dc480609d9c1 Uploaded iuc parents: diff changeset	69 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
2 c838e7136a40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 1 diff changeset	70 <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	71 <output name="output">
dc480609d9c1 Uploaded iuc parents: diff changeset	72 <assert_contents>
dc480609d9c1 Uploaded iuc parents: diff changeset	73 <has_text text="dbNSFP_SIFT_score=0.15" />
dc480609d9c1 Uploaded iuc parents: diff changeset	74 </assert_contents>
dc480609d9c1 Uploaded iuc parents: diff changeset	75 </output>
2 c838e7136a40 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f iuc parents: 1 diff changeset	76 </test> -->
0 dc480609d9c1 Uploaded iuc parents: diff changeset	77 </tests>
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	78 <help><![CDATA[
0 dc480609d9c1 Uploaded iuc parents: diff changeset	79 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.).
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	80 It contains variant annotations such as:
0 dc480609d9c1 Uploaded iuc parents: diff changeset	81
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	82 1000Gp1_AC
0 dc480609d9c1 Uploaded iuc parents: diff changeset	83 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	84 1000Gp1_AF
0 dc480609d9c1 Uploaded iuc parents: diff changeset	85 Alternative allele frequency in the whole 1000Gp1 data
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	86 1000Gp1_AFR_AC
0 dc480609d9c1 Uploaded iuc parents: diff changeset	87 Alternative allele counts in the 1000Gp1 African descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	88 1000Gp1_AFR_AF
0 dc480609d9c1 Uploaded iuc parents: diff changeset	89 Alternative allele frequency in the 1000Gp1 African descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	90 1000Gp1_AMR_AC
0 dc480609d9c1 Uploaded iuc parents: diff changeset	91 Alternative allele counts in the 1000Gp1 American descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	92 1000Gp1_AMR_AF
0 dc480609d9c1 Uploaded iuc parents: diff changeset	93 Alternative allele frequency in the 1000Gp1 American descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	94 1000Gp1_ASN_AC
0 dc480609d9c1 Uploaded iuc parents: diff changeset	95 Alternative allele counts in the 1000Gp1 Asian descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	96 1000Gp1_ASN_AF
0 dc480609d9c1 Uploaded iuc parents: diff changeset	97 Alternative allele frequency in the 1000Gp1 Asian descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	98 1000Gp1_EUR_AC
0 dc480609d9c1 Uploaded iuc parents: diff changeset	99 Alternative allele counts in the 1000Gp1 European descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	100 1000Gp1_EUR_AF
0 dc480609d9c1 Uploaded iuc parents: diff changeset	101 Alternative allele frequency in the 1000Gp1 European descendent samples
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	102 aaalt
0 dc480609d9c1 Uploaded iuc parents: diff changeset	103 Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	104 aapos
0 dc480609d9c1 Uploaded iuc parents: diff changeset	105 Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	106 aapos_SIFT
0 dc480609d9c1 Uploaded iuc parents: diff changeset	107 ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	108 aapos_FATHMM
0 dc480609d9c1 Uploaded iuc parents: diff changeset	109 ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	110 aaref
0 dc480609d9c1 Uploaded iuc parents: diff changeset	111 Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	112 alt
0 dc480609d9c1 Uploaded iuc parents: diff changeset	113 Alternative nucleotide allele (as on the + strand)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	114 Ancestral_allele
0 dc480609d9c1 Uploaded iuc parents: diff changeset	115 Ancestral allele (based on 1000 genomes reference data)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	116 cds_strand
0 dc480609d9c1 Uploaded iuc parents: diff changeset	117 Coding sequence (CDS) strand (+ or -)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	118 chr
0 dc480609d9c1 Uploaded iuc parents: diff changeset	119 Chromosome number
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	120 codonpos
0 dc480609d9c1 Uploaded iuc parents: diff changeset	121 Position on the codon (1, 2 or 3)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	122 Ensembl_geneid
0 dc480609d9c1 Uploaded iuc parents: diff changeset	123 Ensembl gene ID
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	124 Ensembl_transcriptid
0 dc480609d9c1 Uploaded iuc parents: diff changeset	125 Ensembl transcript IDs (separated by ";")
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	126 ESP6500_AA_AF
0 dc480609d9c1 Uploaded iuc parents: diff changeset	127 Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	128 ESP6500_EA_AF
0 dc480609d9c1 Uploaded iuc parents: diff changeset	129 Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	130 FATHMM_pred
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	131 If a FATHMM_score is <=-1.5 (or rankscore <=0.81415) the corresponding non-synonymous SNP is predicted as "D(AMAGING)"; otherwise it is predicted as "T(OLERATED)". Multiple predictions separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	132 FATHMM_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	133 FATHMMori scores were ranked among all FATHMMori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of FATHMMori scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0 to 1
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	134 FATHMM_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	135 FATHMM default score (FATHMMori)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	136 fold-degenerate
0 dc480609d9c1 Uploaded iuc parents: diff changeset	137 Degenerate type (0, 2 or 3)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	138 genename
0 dc480609d9c1 Uploaded iuc parents: diff changeset	139 Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	140 GERP++_NR
0 dc480609d9c1 Uploaded iuc parents: diff changeset	141 GERP++ neutral rate
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	142 GERP++_RS
0 dc480609d9c1 Uploaded iuc parents: diff changeset	143 GERP++ RS score, the larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	144 GERP++_RS_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	145 GERP++ RS scores were ranked among all GERP++ RS scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of GERP++ RS scores in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	146 hg18_pos(1-coor)
0 dc480609d9c1 Uploaded iuc parents: diff changeset	147 Physical position on the chromosome as to hg18 (1-based coordinate)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	148 Interpro_domain
0 dc480609d9c1 Uploaded iuc parents: diff changeset	149 Domain or conserved site on which the variant locates
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	150 LR_pred
0 dc480609d9c1 Uploaded iuc parents: diff changeset	151 Prediction of our LR based ensemble prediction score, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0.5. The rankscore cutoff between "D" and "T" is 0.82268
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	152 LR_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	153 LR scores were ranked among all LR scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of LR scores in dbNSFP. The scores range from 0 to 1
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	154 LR_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	155 Our logistic regression (LR) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from 0 to 1
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	156 LRT_Omega
0 dc480609d9c1 Uploaded iuc parents: diff changeset	157 Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	158 LRT_converted_rankscore
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	159 LRTori scores were first converted as LRTnew=1-LRTori0.5 if Omega<1, or LRTnew=LRTori0.5 if Omega>=1. Then LRTnew scores were ranked among all LRTnew scores in dbNSFP. The rankscore is the ratio of the rank over the total number of the scores in dbNSFP. The scores range from 0.00166 to 0.85682
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	160 LRT_pred
0 dc480609d9c1 Uploaded iuc parents: diff changeset	161 LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	162 LRT_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	163 The original LRT two-sided p-value (LRTori), ranges from 0 to 1
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	164 MutationAssessor_pred
0 dc480609d9c1 Uploaded iuc parents: diff changeset	165 MutationAssessor's functional impact of a variant
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	166 MutationAssessor_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	167 MAori scores were ranked among all MAori scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MAori scores in dbNSFP. The scores range from 0 to 1
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	168 MutationAssessor_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	169 MutationAssessor functional impact combined score (MAori)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	170 MutationTaster_converted_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	171 The MTori scores were first converted: if the prediction is "A" or "D" MTnew=MTori; if the prediction is "N" or "P", MTnew=1-MTori. Then MTnew scores were ranked among all MTnew scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of MTnew scores in dbNSFP. The scores range from 0.0931 to 0.80722
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	172 MutationTaster_pred
0 dc480609d9c1 Uploaded iuc parents: diff changeset	173 MutationTaster prediction
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	174 MutationTaster_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	175 MutationTaster p-value (MTori), ranges from 0 to 1
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	176 phastCons46way_placental
0 dc480609d9c1 Uploaded iuc parents: diff changeset	177 phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	178 phastCons46way_placental_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	179 phastCons46way_placental scores were ranked among all phastCons46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_placental scores in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	180 phastCons46way_primate
0 dc480609d9c1 Uploaded iuc parents: diff changeset	181 phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	182 phastCons46way_primate_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	183 phastCons46way_primate scores were ranked among all phastCons46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons46way_primate scores in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	184 phastCons100way_vertebrate
0 dc480609d9c1 Uploaded iuc parents: diff changeset	185 phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	186 phastCons100way_vertebrate_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	187 phastCons100way_vertebrate scores were ranked among all phastCons100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phastCons100way_vertebrate scores in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	188 phyloP46way_placental
0 dc480609d9c1 Uploaded iuc parents: diff changeset	189 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	190 phyloP46way_placental_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	191 phyloP46way_placental scores were ranked among all phyloP46way_placental scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_placental scores in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	192 phyloP46way_primate
0 dc480609d9c1 Uploaded iuc parents: diff changeset	193 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	194 phyloP46way_primate_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	195 phyloP46way_primate scores were ranked among all phyloP46way_primate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP46way_primate scores in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	196 phyloP100way_vertebrate
0 dc480609d9c1 Uploaded iuc parents: diff changeset	197 phyloP (phylogenetic p-values) conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	198 phyloP100way_vertebrate_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	199 phyloP100way_vertebrate scores were ranked among all phyloP100way_vertebrate scores in dbNSFP. The rankscore is the ratio of the rank of the score over the total number of phyloP100way_vertebrate scores in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	200 Polyphen2_HDIV_pred
0 dc480609d9c1 Uploaded iuc parents: diff changeset	201 Polyphen2 prediction based on HumDiv
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	202 Polyphen2_HDIV_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	203 Polyphen2 HDIV scores were first ranked among all HDIV scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.02656 to 0.89917
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	204 Polyphen2_HDIV_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	205 Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	206 Polyphen2_HVAR_pred
0 dc480609d9c1 Uploaded iuc parents: diff changeset	207 Polyphen2 prediction based on HumVar
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	208 Polyphen2_HVAR_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	209 Polyphen2 HVAR scores were first ranked among all HVAR scores in dbNSFP. The rankscore is the ratio of the rank the score over the total number of the scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The scores range from 0.01281 to 0.9711
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	210 Polyphen2_HVAR_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	211 Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	212 pos(1-coor)
0 dc480609d9c1 Uploaded iuc parents: diff changeset	213 Physical position on the chromosome as to hg19 (1-based coordinate)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	214 RadialSVM_pred
0 dc480609d9c1 Uploaded iuc parents: diff changeset	215 Prediction of our SVM based ensemble prediction score, "T(olerated)" or "D(amaging)". The score cutoff between "D" and "T" is 0. The rankscore cutoff between "D" and "T" is 0.83357
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	216 RadialSVM_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	217 RadialSVM scores were ranked among all RadialSVM scores in dbNSFP. The rankscore is the ratio of the rank of the screo over the total number of RadialSVM scores in dbNSFP. The scores range from 0 to 1
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	218 RadialSVM_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	219 Our support vector machine (SVM) based ensemble prediction score, which incorporated 10 scores (SIFT, PolyPhen-2 HDIV, PolyPhen-2 HVAR, GERP++, MutationTaster, Mutation Assessor, FATHMM, LRT, SiPhy, PhyloP) and the maximum frequency observed in the 1000 genomes populations. Larger value means the SNV is more likely to be damaging. Scores range from -2 to 3 in dbNSFP
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	220 ref
0 dc480609d9c1 Uploaded iuc parents: diff changeset	221 Reference nucleotide allele (as on the + strand)
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	222 refcodon
0 dc480609d9c1 Uploaded iuc parents: diff changeset	223 Reference codon
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	224 Reliability_index
0 dc480609d9c1 Uploaded iuc parents: diff changeset	225 Number of observed component scores (except the maximum frequency in the 1000 genomes populations) for RadialSVM and LR. Ranges from 1 to 10. As RadialSVM and LR scores are calculated based on imputed data, the less missing component scores, the higher the reliability of the scores and predictions
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	226 SIFT_converted_rankscore
0 dc480609d9c1 Uploaded iuc parents: diff changeset	227 SIFTori scores were first converted to SIFTnew=1-SIFTori, then ranked among all SIFTnew scores in dbNSFP. The rankscore is the ratio of the rank the SIFTnew score over the total number of SIFTnew scores in dbNSFP. If there are multiple scores, only the most damaging (largest) rankscore is presented. The rankscores range from 0.02654 to 0.87932
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	228 SIFT_pred
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	229 If SIFTori is smaller than 0.05 (rankscore>0.55) the corresponding non-synonymous SNP is predicted as "D(amaging)"; otherwise it is predicted as "T(olerated)". Multiple predictions separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	230 SIFT_score
0 dc480609d9c1 Uploaded iuc parents: diff changeset	231 SIFT score (SIFTori). Scores range from 0 to 1. The smaller the score the more likely the SNP has damaging effect. Multiple scores separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	232 SiPhy_29way_logOdds
0 dc480609d9c1 Uploaded iuc parents: diff changeset	233 SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	234 SiPhy_29way_pi
0 dc480609d9c1 Uploaded iuc parents: diff changeset	235 The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	236 SLR_test_statistic
0 dc480609d9c1 Uploaded iuc parents: diff changeset	237 SLR test statistic for testing natural selection on codons. A negative value indicates negative selection, and a positive value indicates positive selection. Larger magnitude of the value suggests stronger evidence
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	238 Uniprot_aapos
0 dc480609d9c1 Uploaded iuc parents: diff changeset	239 Amino acid position as to Uniprot. Multiple entries separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	240 Uniprot_acc
0 dc480609d9c1 Uploaded iuc parents: diff changeset	241 Uniprot accession number. Multiple entries separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	242 Uniprot_id
0 dc480609d9c1 Uploaded iuc parents: diff changeset	243 Uniprot ID number. Multiple entries separated by ";"
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	244 UniSNP_ids
0 dc480609d9c1 Uploaded iuc parents: diff changeset	245 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;...
dc480609d9c1 Uploaded iuc parents: diff changeset	246
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	247 The dbNSFP database is available from https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human genome builds.
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	248
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	249 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp and a couple of prebuilt dbNSFP databases are available at:
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	250 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
0 dc480609d9c1 Uploaded iuc parents: diff changeset	251
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	252 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	253
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	254 - The first line of the file must be column headers that name the annotations.
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	255 - The first 4 columns are required and must be:
0 dc480609d9c1 Uploaded iuc parents: diff changeset	256
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	257 1. chr: chromosome
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	258 2. pos(1-coor): position in chromosome
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	259 3. ref: reference base
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	260 4. alt: alternate base
0 dc480609d9c1 Uploaded iuc parents: diff changeset	261
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	262 For example::
0 dc480609d9c1 Uploaded iuc parents: diff changeset	263
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	264 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	265 1 69134 A C E A OR4F5 0.03
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	266 1 69134 A G E G OR4F5 0.09
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	267 1 69134 A T E V OR4F5 0.03
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	268 4 100239319 T A H L ADH1B 0
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	269 4 100239319 T C H R ADH1B 0.15
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	270 4 100239319 T G H P ADH1B 0
0 dc480609d9c1 Uploaded iuc parents: diff changeset	271
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	272 The Galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:
0 dc480609d9c1 Uploaded iuc parents: diff changeset	273
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	274 1. Upload the tabular file, set the datatype as: "dbnsfp.tabular"
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	275 2. Edit the history dataset attributes (pencil icon): Use "Convert Format" to convert the "dbnsfp.tabular" to the correct format for SnpSift dbnsfp: "snpsiftdbnsfp".
0 dc480609d9c1 Uploaded iuc parents: diff changeset	276
dc480609d9c1 Uploaded iuc parents: diff changeset	277 @EXTERNAL_DOCUMENTATION@
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	278 - http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	279 ]]></help>
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	280 <expand macro="citations">
4 4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	281 <citation type="doi">10.1002/humu.21517</citation>
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	282 <citation type="doi">10.1002/humu.22932</citation>
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	283 <citation type="doi">10.1093/hmg/ddu733</citation>
4e21e4f2bc48 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit fbc18d9128669e461e76ed13307ee88dd774afa5 iuc parents: 2 diff changeset	284 <citation type="doi">10.3389/fgene.2012.00035</citation>
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	285 </expand>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	286 </tool>

Mercurial > repos > iuc > snpsift_dbnsfp

annotate snpSift_dbnsfp.xml @ 4:4e21e4f2bc48 draft default tip