snpsift_dbnsfp: snpSift_dbnsfp.xml annotate

annotate snpSift_dbnsfp.xml @ 2:c838e7136a40 draft

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

author	iuc
date	Mon, 05 Dec 2016 12:06:13 -0500
parents	13191d4914f7
children	4e21e4f2bc48

rev	line source
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	1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1">
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	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[
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	10 @CONDA_SNPSIFT_JAR_PATH@ &&
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	11 java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp -v
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	12 #if $db.dbsrc == 'cached':
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	13 -db "$db.dbnsfp"
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	14 #if $db.annotations and str($db.annotations) != '':
0 dc480609d9c1 Uploaded iuc parents: diff changeset	15 -f "$db.annotations"
dc480609d9c1 Uploaded iuc parents: diff changeset	16 #end if
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	17 #else:
0 dc480609d9c1 Uploaded iuc parents: diff changeset	18 -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}"
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	19 #if $db.annotations and str($db.annotations) != '':
0 dc480609d9c1 Uploaded iuc parents: diff changeset	20 -f "$db.annotations"
dc480609d9c1 Uploaded iuc parents: diff changeset	21 #end if
1 13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	22 #end if
13191d4914f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31 iuc parents: 0 diff changeset	23 "$input" > "$output"
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	24 2> tmp.err && grep -v file tmp.err
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	25 ]]>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	26 </command>
dc480609d9c1 Uploaded iuc parents: diff changeset	27 <inputs>
dc480609d9c1 Uploaded iuc parents: diff changeset	28 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
dc480609d9c1 Uploaded iuc parents: diff changeset	29 <conditional name="db">
dc480609d9c1 Uploaded iuc parents: diff changeset	30 <param name="dbsrc" type="select" label="dbNSFP ">
dc480609d9c1 Uploaded iuc parents: diff changeset	31 <option value="cached">Locally installed dbNSFP database </option>
dc480609d9c1 Uploaded iuc parents: diff changeset	32 <option value="history">dbNSFP database from your history</option>
dc480609d9c1 Uploaded iuc parents: diff changeset	33 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	34 <when value="cached">
dc480609d9c1 Uploaded iuc parents: diff changeset	35 <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	36 <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	37 <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	38 <column name="value" index="3"/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	39 </options>
dc480609d9c1 Uploaded iuc parents: diff changeset	40 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	41 <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	42 <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	43 <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	44 <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	45 <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	46 <filter type="multiple_splitter" column="4" separator=","/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	47 </options>
dc480609d9c1 Uploaded iuc parents: diff changeset	48 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	49 </when>
dc480609d9c1 Uploaded iuc parents: diff changeset	50 <when value="history">
dc480609d9c1 Uploaded iuc parents: diff changeset	51 <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/>
dc480609d9c1 Uploaded iuc parents: diff changeset	52 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with">
dc480609d9c1 Uploaded iuc parents: diff changeset	53 <options>
dc480609d9c1 Uploaded iuc parents: diff changeset	54 <filter type="data_meta" ref="dbnsfpdb" key="annotation" />
dc480609d9c1 Uploaded iuc parents: diff changeset	55 </options>
dc480609d9c1 Uploaded iuc parents: diff changeset	56 </param>
dc480609d9c1 Uploaded iuc parents: diff changeset	57 </when>
dc480609d9c1 Uploaded iuc parents: diff changeset	58 </conditional>
dc480609d9c1 Uploaded iuc parents: diff changeset	59 </inputs>
dc480609d9c1 Uploaded iuc parents: diff changeset	60 <outputs>
dc480609d9c1 Uploaded iuc parents: diff changeset	61 <data format="vcf" name="output" />
dc480609d9c1 Uploaded iuc parents: diff changeset	62 </outputs>
dc480609d9c1 Uploaded iuc parents: diff changeset	63 <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	64 <!-- 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	65 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	66 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	67 until after the conversion is completed.
0 dc480609d9c1 Uploaded iuc parents: diff changeset	68 <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	69 <param name="input" ftype="vcf" value="test_annotate_in.vcf"/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	70 <param name="dbsrc" value="history"/>
dc480609d9c1 Uploaded iuc parents: diff changeset	71 <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	72 <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	73 <output name="output">
dc480609d9c1 Uploaded iuc parents: diff changeset	74 <assert_contents>
dc480609d9c1 Uploaded iuc parents: diff changeset	75 <has_text text="dbNSFP_SIFT_score=0.15" />
dc480609d9c1 Uploaded iuc parents: diff changeset	76 </assert_contents>
dc480609d9c1 Uploaded iuc parents: diff changeset	77 </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	78 </test> -->
0 dc480609d9c1 Uploaded iuc parents: diff changeset	79 </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	80 <help><![CDATA[
0 dc480609d9c1 Uploaded iuc parents: diff changeset	81
dc480609d9c1 Uploaded iuc parents: diff changeset	82 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	83 It contains variant annotations such as:
0 dc480609d9c1 Uploaded iuc parents: diff changeset	84
dc480609d9c1 Uploaded iuc parents: diff changeset	85
dc480609d9c1 Uploaded iuc parents: diff changeset	86 1000Gp1_AC
dc480609d9c1 Uploaded iuc parents: diff changeset	87 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data
dc480609d9c1 Uploaded iuc parents: diff changeset	88 1000Gp1_AF
dc480609d9c1 Uploaded iuc parents: diff changeset	89 Alternative allele frequency in the whole 1000Gp1 data
dc480609d9c1 Uploaded iuc parents: diff changeset	90 1000Gp1_AFR_AC
dc480609d9c1 Uploaded iuc parents: diff changeset	91 Alternative allele counts in the 1000Gp1 African descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	92 1000Gp1_AFR_AF
dc480609d9c1 Uploaded iuc parents: diff changeset	93 Alternative allele frequency in the 1000Gp1 African descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	94 1000Gp1_AMR_AC
dc480609d9c1 Uploaded iuc parents: diff changeset	95 Alternative allele counts in the 1000Gp1 American descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	96 1000Gp1_AMR_AF
dc480609d9c1 Uploaded iuc parents: diff changeset	97 Alternative allele frequency in the 1000Gp1 American descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	98 1000Gp1_ASN_AC
dc480609d9c1 Uploaded iuc parents: diff changeset	99 Alternative allele counts in the 1000Gp1 Asian descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	100 1000Gp1_ASN_AF
dc480609d9c1 Uploaded iuc parents: diff changeset	101 Alternative allele frequency in the 1000Gp1 Asian descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	102 1000Gp1_EUR_AC
dc480609d9c1 Uploaded iuc parents: diff changeset	103 Alternative allele counts in the 1000Gp1 European descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	104 1000Gp1_EUR_AF
dc480609d9c1 Uploaded iuc parents: diff changeset	105 Alternative allele frequency in the 1000Gp1 European descendent samples
dc480609d9c1 Uploaded iuc parents: diff changeset	106 aaalt
dc480609d9c1 Uploaded iuc parents: diff changeset	107 Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
dc480609d9c1 Uploaded iuc parents: diff changeset	108 aapos
dc480609d9c1 Uploaded iuc parents: diff changeset	109 Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron)
dc480609d9c1 Uploaded iuc parents: diff changeset	110 aapos_SIFT
dc480609d9c1 Uploaded iuc parents: diff changeset	111 ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	112 aapos_FATHMM
dc480609d9c1 Uploaded iuc parents: diff changeset	113 ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	114 aaref
dc480609d9c1 Uploaded iuc parents: diff changeset	115 Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron)
dc480609d9c1 Uploaded iuc parents: diff changeset	116 alt
dc480609d9c1 Uploaded iuc parents: diff changeset	117 Alternative nucleotide allele (as on the + strand)
dc480609d9c1 Uploaded iuc parents: diff changeset	118 Ancestral_allele
dc480609d9c1 Uploaded iuc parents: diff changeset	119 Ancestral allele (based on 1000 genomes reference data)
dc480609d9c1 Uploaded iuc parents: diff changeset	120 cds_strand
dc480609d9c1 Uploaded iuc parents: diff changeset	121 Coding sequence (CDS) strand (+ or -)
dc480609d9c1 Uploaded iuc parents: diff changeset	122 chr
dc480609d9c1 Uploaded iuc parents: diff changeset	123 Chromosome number
dc480609d9c1 Uploaded iuc parents: diff changeset	124 codonpos
dc480609d9c1 Uploaded iuc parents: diff changeset	125 Position on the codon (1, 2 or 3)
dc480609d9c1 Uploaded iuc parents: diff changeset	126 Ensembl_geneid
dc480609d9c1 Uploaded iuc parents: diff changeset	127 Ensembl gene ID
dc480609d9c1 Uploaded iuc parents: diff changeset	128 Ensembl_transcriptid
dc480609d9c1 Uploaded iuc parents: diff changeset	129 Ensembl transcript IDs (separated by ";")
dc480609d9c1 Uploaded iuc parents: diff changeset	130 ESP6500_AA_AF
dc480609d9c1 Uploaded iuc parents: diff changeset	131 Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
dc480609d9c1 Uploaded iuc parents: diff changeset	132 ESP6500_EA_AF
dc480609d9c1 Uploaded iuc parents: diff changeset	133 Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set)
dc480609d9c1 Uploaded iuc parents: diff changeset	134 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	135 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 ";"
0 dc480609d9c1 Uploaded iuc parents: diff changeset	136 FATHMM_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	137 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
dc480609d9c1 Uploaded iuc parents: diff changeset	138 FATHMM_score
dc480609d9c1 Uploaded iuc parents: diff changeset	139 FATHMM default score (FATHMMori)
dc480609d9c1 Uploaded iuc parents: diff changeset	140 fold-degenerate
dc480609d9c1 Uploaded iuc parents: diff changeset	141 Degenerate type (0, 2 or 3)
dc480609d9c1 Uploaded iuc parents: diff changeset	142 genename
dc480609d9c1 Uploaded iuc parents: diff changeset	143 Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	144 GERP++_NR
dc480609d9c1 Uploaded iuc parents: diff changeset	145 GERP++ neutral rate
dc480609d9c1 Uploaded iuc parents: diff changeset	146 GERP++_RS
dc480609d9c1 Uploaded iuc parents: diff changeset	147 GERP++ RS score, the larger the score, the more conserved the site
dc480609d9c1 Uploaded iuc parents: diff changeset	148 GERP++_RS_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	149 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
dc480609d9c1 Uploaded iuc parents: diff changeset	150 hg18_pos(1-coor)
dc480609d9c1 Uploaded iuc parents: diff changeset	151 Physical position on the chromosome as to hg18 (1-based coordinate)
dc480609d9c1 Uploaded iuc parents: diff changeset	152 Interpro_domain
dc480609d9c1 Uploaded iuc parents: diff changeset	153 Domain or conserved site on which the variant locates
dc480609d9c1 Uploaded iuc parents: diff changeset	154 LR_pred
dc480609d9c1 Uploaded iuc parents: diff changeset	155 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
dc480609d9c1 Uploaded iuc parents: diff changeset	156 LR_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	157 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
dc480609d9c1 Uploaded iuc parents: diff changeset	158 LR_score
dc480609d9c1 Uploaded iuc parents: diff changeset	159 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
dc480609d9c1 Uploaded iuc parents: diff changeset	160 LRT_Omega
dc480609d9c1 Uploaded iuc parents: diff changeset	161 Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT)
dc480609d9c1 Uploaded iuc parents: diff changeset	162 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	163 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
0 dc480609d9c1 Uploaded iuc parents: diff changeset	164 LRT_pred
dc480609d9c1 Uploaded iuc parents: diff changeset	165 LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score
dc480609d9c1 Uploaded iuc parents: diff changeset	166 LRT_score
dc480609d9c1 Uploaded iuc parents: diff changeset	167 The original LRT two-sided p-value (LRTori), ranges from 0 to 1
dc480609d9c1 Uploaded iuc parents: diff changeset	168 MutationAssessor_pred
dc480609d9c1 Uploaded iuc parents: diff changeset	169 MutationAssessor's functional impact of a variant
dc480609d9c1 Uploaded iuc parents: diff changeset	170 MutationAssessor_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	171 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
dc480609d9c1 Uploaded iuc parents: diff changeset	172 MutationAssessor_score
dc480609d9c1 Uploaded iuc parents: diff changeset	173 MutationAssessor functional impact combined score (MAori)
dc480609d9c1 Uploaded iuc parents: diff changeset	174 MutationTaster_converted_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	175 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
dc480609d9c1 Uploaded iuc parents: diff changeset	176 MutationTaster_pred
dc480609d9c1 Uploaded iuc parents: diff changeset	177 MutationTaster prediction
dc480609d9c1 Uploaded iuc parents: diff changeset	178 MutationTaster_score
dc480609d9c1 Uploaded iuc parents: diff changeset	179 MutationTaster p-value (MTori), ranges from 0 to 1
dc480609d9c1 Uploaded iuc parents: diff changeset	180 phastCons46way_placental
dc480609d9c1 Uploaded iuc parents: diff changeset	181 phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site
dc480609d9c1 Uploaded iuc parents: diff changeset	182 phastCons46way_placental_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	183 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
dc480609d9c1 Uploaded iuc parents: diff changeset	184 phastCons46way_primate
dc480609d9c1 Uploaded iuc parents: diff changeset	185 phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site
dc480609d9c1 Uploaded iuc parents: diff changeset	186 phastCons46way_primate_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	187 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
dc480609d9c1 Uploaded iuc parents: diff changeset	188 phastCons100way_vertebrate
dc480609d9c1 Uploaded iuc parents: diff changeset	189 phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site
dc480609d9c1 Uploaded iuc parents: diff changeset	190 phastCons100way_vertebrate_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	191 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
dc480609d9c1 Uploaded iuc parents: diff changeset	192 phyloP46way_placental
dc480609d9c1 Uploaded iuc parents: diff changeset	193 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
dc480609d9c1 Uploaded iuc parents: diff changeset	194 phyloP46way_placental_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	195 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
dc480609d9c1 Uploaded iuc parents: diff changeset	196 phyloP46way_primate
dc480609d9c1 Uploaded iuc parents: diff changeset	197 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
dc480609d9c1 Uploaded iuc parents: diff changeset	198 phyloP46way_primate_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	199 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
dc480609d9c1 Uploaded iuc parents: diff changeset	200 phyloP100way_vertebrate
dc480609d9c1 Uploaded iuc parents: diff changeset	201 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
dc480609d9c1 Uploaded iuc parents: diff changeset	202 phyloP100way_vertebrate_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	203 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
dc480609d9c1 Uploaded iuc parents: diff changeset	204 Polyphen2_HDIV_pred
dc480609d9c1 Uploaded iuc parents: diff changeset	205 Polyphen2 prediction based on HumDiv
dc480609d9c1 Uploaded iuc parents: diff changeset	206 Polyphen2_HDIV_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	207 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
dc480609d9c1 Uploaded iuc parents: diff changeset	208 Polyphen2_HDIV_score
dc480609d9c1 Uploaded iuc parents: diff changeset	209 Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	210 Polyphen2_HVAR_pred
dc480609d9c1 Uploaded iuc parents: diff changeset	211 Polyphen2 prediction based on HumVar
dc480609d9c1 Uploaded iuc parents: diff changeset	212 Polyphen2_HVAR_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	213 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
dc480609d9c1 Uploaded iuc parents: diff changeset	214 Polyphen2_HVAR_score
dc480609d9c1 Uploaded iuc parents: diff changeset	215 Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	216 pos(1-coor)
dc480609d9c1 Uploaded iuc parents: diff changeset	217 Physical position on the chromosome as to hg19 (1-based coordinate)
dc480609d9c1 Uploaded iuc parents: diff changeset	218 RadialSVM_pred
dc480609d9c1 Uploaded iuc parents: diff changeset	219 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
dc480609d9c1 Uploaded iuc parents: diff changeset	220 RadialSVM_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	221 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
dc480609d9c1 Uploaded iuc parents: diff changeset	222 RadialSVM_score
dc480609d9c1 Uploaded iuc parents: diff changeset	223 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
dc480609d9c1 Uploaded iuc parents: diff changeset	224 ref
dc480609d9c1 Uploaded iuc parents: diff changeset	225 Reference nucleotide allele (as on the + strand)
dc480609d9c1 Uploaded iuc parents: diff changeset	226 refcodon
dc480609d9c1 Uploaded iuc parents: diff changeset	227 Reference codon
dc480609d9c1 Uploaded iuc parents: diff changeset	228 Reliability_index
dc480609d9c1 Uploaded iuc parents: diff changeset	229 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
dc480609d9c1 Uploaded iuc parents: diff changeset	230 SIFT_converted_rankscore
dc480609d9c1 Uploaded iuc parents: diff changeset	231 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
dc480609d9c1 Uploaded iuc parents: diff changeset	232 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	233 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 ";"
0 dc480609d9c1 Uploaded iuc parents: diff changeset	234 SIFT_score
dc480609d9c1 Uploaded iuc parents: diff changeset	235 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 ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	236 SiPhy_29way_logOdds
dc480609d9c1 Uploaded iuc parents: diff changeset	237 SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site
dc480609d9c1 Uploaded iuc parents: diff changeset	238 SiPhy_29way_pi
dc480609d9c1 Uploaded iuc parents: diff changeset	239 The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes
dc480609d9c1 Uploaded iuc parents: diff changeset	240 SLR_test_statistic
dc480609d9c1 Uploaded iuc parents: diff changeset	241 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
dc480609d9c1 Uploaded iuc parents: diff changeset	242 Uniprot_aapos
dc480609d9c1 Uploaded iuc parents: diff changeset	243 Amino acid position as to Uniprot. Multiple entries separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	244 Uniprot_acc
dc480609d9c1 Uploaded iuc parents: diff changeset	245 Uniprot accession number. Multiple entries separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	246 Uniprot_id
dc480609d9c1 Uploaded iuc parents: diff changeset	247 Uniprot ID number. Multiple entries separated by ";"
dc480609d9c1 Uploaded iuc parents: diff changeset	248 UniSNP_ids
dc480609d9c1 Uploaded iuc parents: diff changeset	249 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	250
dc480609d9c1 Uploaded iuc parents: diff changeset	251
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	252 The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human genome builds.
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	253
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	254 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation:
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	255 ( It also provides links for dbNSFP databases prebuilt for SnpSift )
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	256 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
0 dc480609d9c1 Uploaded iuc parents: diff changeset	257
dc480609d9c1 Uploaded iuc parents: diff changeset	258 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has::
dc480609d9c1 Uploaded iuc parents: diff changeset	259
dc480609d9c1 Uploaded iuc parents: diff changeset	260 - The first line of the file must be column headers that name the annotations.
dc480609d9c1 Uploaded iuc parents: diff changeset	261 - The first 4 columns are required and must be::
dc480609d9c1 Uploaded iuc parents: diff changeset	262 1. chromosome
dc480609d9c1 Uploaded iuc parents: diff changeset	263 2. position in chromosome
dc480609d9c1 Uploaded iuc parents: diff changeset	264 3. reference base
dc480609d9c1 Uploaded iuc parents: diff changeset	265 4. alternate base
dc480609d9c1 Uploaded iuc parents: diff changeset	266
dc480609d9c1 Uploaded iuc parents: diff changeset	267 For example:
dc480609d9c1 Uploaded iuc parents: diff changeset	268
dc480609d9c1 Uploaded iuc parents: diff changeset	269 ::
dc480609d9c1 Uploaded iuc parents: diff changeset	270
dc480609d9c1 Uploaded iuc parents: diff changeset	271 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score
dc480609d9c1 Uploaded iuc parents: diff changeset	272 1 69134 A C E A OR4F5 0.03
dc480609d9c1 Uploaded iuc parents: diff changeset	273 1 69134 A G E G OR4F5 0.09
dc480609d9c1 Uploaded iuc parents: diff changeset	274 1 69134 A T E V OR4F5 0.03
dc480609d9c1 Uploaded iuc parents: diff changeset	275 4 100239319 T A H L ADH1B 0
dc480609d9c1 Uploaded iuc parents: diff changeset	276 4 100239319 T C H R ADH1B 0.15
dc480609d9c1 Uploaded iuc parents: diff changeset	277 4 100239319 T G H P ADH1B 0
dc480609d9c1 Uploaded iuc parents: diff changeset	278
dc480609d9c1 Uploaded iuc parents: diff changeset	279
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 The galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP:
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	281 1. Upload the tabular file, set the datatype as: "dbnsfp.tabular"
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	282 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	283
dc480609d9c1 Uploaded iuc parents: diff changeset	284
dc480609d9c1 Uploaded iuc parents: diff changeset	285 @EXTERNAL_DOCUMENTATION@
dc480609d9c1 Uploaded iuc parents: diff changeset	286 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
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	287 ]]>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	288 </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	289 <expand macro="citations">
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	290 <citation type="doi">DOI: 10.1002/humu.21517</citation>
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	291 <citation type="doi">DOI: 10.1002/humu.22376</citation>
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	292 <citation type="doi">DOI: 10.1002/humu.22932</citation>
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	293 <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
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	294 <citation type="doi">doi: 10.1093/nar/gku1206</citation>
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	295 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
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	296 </expand>
0 dc480609d9c1 Uploaded iuc parents: diff changeset	297 </tool>

Mercurial > repos > iuc > snpsift_dbnsfp

annotate snpSift_dbnsfp.xml @ 2:c838e7136a40 draft