Mercurial > repos > iuc > snpsift_dbnsfp
annotate snpSift_dbnsfp.xml @ 1:13191d4914f7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 10:04:48 -0400 |
| parents | dc480609d9c1 |
| children | c838e7136a40 |
| rev | line source |
|---|---|
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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1 <tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0"> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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2 <description>Add Annotations from dbNSFP or similar annotation DBs</description> |
| 0 | 3 <macros> |
| 4 <import>snpSift_macros.xml</import> | |
| 5 </macros> | |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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6 <expand macro="requirements" /> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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7 <expand macro="stdio" /> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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8 <expand macro="version_command" /> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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9 <command><![CDATA[ |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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10 java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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11 #if $db.dbsrc == 'cached': |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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12 -db "$db.dbnsfp" |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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13 #if $db.annotations and str($db.annotations) != '': |
| 0 | 14 -f "$db.annotations" |
| 15 #end if | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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16 #else: |
| 0 | 17 -db "${db.dbnsfpdb.extra_files_path}/${db.dbnsfpdb.metadata.bgzip}" |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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18 #if $db.annotations and str($db.annotations) != '': |
| 0 | 19 -f "$db.annotations" |
| 20 #end if | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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21 #end if |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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22 "$input" > "$output" |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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23 2> tmp.err && grep -v file tmp.err |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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24 ]]> |
| 0 | 25 </command> |
| 26 <inputs> | |
| 27 <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/> | |
| 28 <conditional name="db"> | |
| 29 <param name="dbsrc" type="select" label="dbNSFP "> | |
| 30 <option value="cached">Locally installed dbNSFP database </option> | |
| 31 <option value="history">dbNSFP database from your history</option> | |
| 32 </param> | |
| 33 <when value="cached"> | |
| 34 <param name="dbnsfp" type="select" label="Genome"> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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35 <options from_data_table="snpsift_dbnsfps"> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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36 <column name="name" index="2"/> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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37 <column name="value" index="3"/> |
| 0 | 38 </options> |
| 39 </param> | |
| 40 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with"> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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41 <options from_data_table="snpsift_dbnsfps"> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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42 <column name="name" index="4"/> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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changeset
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43 <column name="value" index="4"/> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
iuc
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changeset
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44 <filter type="param_value" ref="dbnsfp" column="3" /> |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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45 <filter type="multiple_splitter" column="4" separator=","/> |
| 0 | 46 </options> |
| 47 </param> | |
| 48 </when> | |
| 49 <when value="history"> | |
| 50 <param name="dbnsfpdb" type="data" format="snpsiftdbnsfp" label="DbNSFP"/> | |
| 51 <param name="annotations" type="select" multiple="true" display="checkboxes" label="Annotate with"> | |
| 52 <options> | |
| 53 <filter type="data_meta" ref="dbnsfpdb" key="annotation" /> | |
| 54 </options> | |
| 55 </param> | |
| 56 </when> | |
| 57 </conditional> | |
| 58 </inputs> | |
| 59 <outputs> | |
| 60 <data format="vcf" name="output" /> | |
| 61 </outputs> | |
| 62 <tests> | |
| 63 <test> | |
| 64 <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/> | |
| 65 <param name="dbsrc" value="history"/> | |
| 66 <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" /> | |
| 67 <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/> | |
| 68 <output name="output"> | |
| 69 <assert_contents> | |
| 70 <has_text text="dbNSFP_SIFT_score=0.15" /> | |
| 71 </assert_contents> | |
| 72 </output> | |
| 73 </test> | |
| 74 </tests> | |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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75 <help><![CDATA[ |
| 0 | 76 |
| 77 The dbNSFP is an integrated database of functional predictions from multiple algorithms (SIFT, Polyphen2, LRT and MutationTaster, PhyloP and GERP++, etc.). | |
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13191d4914f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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78 It contains variant annotations such as: |
| 0 | 79 |
| 80 | |
| 81 1000Gp1_AC | |
| 82 Alternative allele counts in the whole 1000 genomes phase 1 (1000Gp1) data | |
| 83 1000Gp1_AF | |
| 84 Alternative allele frequency in the whole 1000Gp1 data | |
| 85 1000Gp1_AFR_AC | |
| 86 Alternative allele counts in the 1000Gp1 African descendent samples | |
| 87 1000Gp1_AFR_AF | |
| 88 Alternative allele frequency in the 1000Gp1 African descendent samples | |
| 89 1000Gp1_AMR_AC | |
| 90 Alternative allele counts in the 1000Gp1 American descendent samples | |
| 91 1000Gp1_AMR_AF | |
| 92 Alternative allele frequency in the 1000Gp1 American descendent samples | |
| 93 1000Gp1_ASN_AC | |
| 94 Alternative allele counts in the 1000Gp1 Asian descendent samples | |
| 95 1000Gp1_ASN_AF | |
| 96 Alternative allele frequency in the 1000Gp1 Asian descendent samples | |
| 97 1000Gp1_EUR_AC | |
| 98 Alternative allele counts in the 1000Gp1 European descendent samples | |
| 99 1000Gp1_EUR_AF | |
| 100 Alternative allele frequency in the 1000Gp1 European descendent samples | |
| 101 aaalt | |
| 102 Alternative amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron) | |
| 103 aapos | |
| 104 Amino acid position as to the protein. "-1" if the variant is a splicing site SNP (2bp on each end of an intron) | |
| 105 aapos_SIFT | |
| 106 ENSP id and amino acid positions corresponding to SIFT scores. Multiple entries separated by ";" | |
| 107 aapos_FATHMM | |
| 108 ENSP id and amino acid positions corresponding to FATHMM scores. Multiple entries separated by ";" | |
| 109 aaref | |
| 110 Reference amino acid. "." if the variant is a splicing site SNP (2bp on each end of an intron) | |
| 111 alt | |
| 112 Alternative nucleotide allele (as on the + strand) | |
| 113 Ancestral_allele | |
| 114 Ancestral allele (based on 1000 genomes reference data) | |
| 115 cds_strand | |
| 116 Coding sequence (CDS) strand (+ or -) | |
| 117 chr | |
| 118 Chromosome number | |
| 119 codonpos | |
| 120 Position on the codon (1, 2 or 3) | |
| 121 Ensembl_geneid | |
| 122 Ensembl gene ID | |
| 123 Ensembl_transcriptid | |
| 124 Ensembl transcript IDs (separated by ";") | |
| 125 ESP6500_AA_AF | |
| 126 Alternative allele frequency in the African American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set) | |
| 127 ESP6500_EA_AF | |
| 128 Alternative allele frequency in the European American samples of the NHLBI GO Exome Sequencing Project (ESP6500 data set) | |
| 129 FATHMM_pred | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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130 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 | 131 FATHMM_rankscore |
| 132 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 | |
| 133 FATHMM_score | |
| 134 FATHMM default score (FATHMMori) | |
| 135 fold-degenerate | |
| 136 Degenerate type (0, 2 or 3) | |
| 137 genename | |
| 138 Gene name; if the non-synonymous SNP can be assigned to multiple genes, gene names are separated by ";" | |
| 139 GERP++_NR | |
| 140 GERP++ neutral rate | |
| 141 GERP++_RS | |
| 142 GERP++ RS score, the larger the score, the more conserved the site | |
| 143 GERP++_RS_rankscore | |
| 144 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 | |
| 145 hg18_pos(1-coor) | |
| 146 Physical position on the chromosome as to hg18 (1-based coordinate) | |
| 147 Interpro_domain | |
| 148 Domain or conserved site on which the variant locates | |
| 149 LR_pred | |
| 150 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 | |
| 151 LR_rankscore | |
| 152 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 | |
| 153 LR_score | |
| 154 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 | |
| 155 LRT_Omega | |
| 156 Estimated nonsynonymous-to-synonymous-rate ratio (Omega, reported by LRT) | |
| 157 LRT_converted_rankscore | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit 21b46ae2c90ba7e569b2b3a9eaf938f8dedb2c31
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158 LRTori scores were first converted as LRTnew=1-LRTori*0.5 if Omega<1, or LRTnew=LRTori*0.5 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 | 159 LRT_pred |
| 160 LRT prediction, D(eleterious), N(eutral) or U(nknown), which is not solely determined by the score | |
| 161 LRT_score | |
| 162 The original LRT two-sided p-value (LRTori), ranges from 0 to 1 | |
| 163 MutationAssessor_pred | |
| 164 MutationAssessor's functional impact of a variant | |
| 165 MutationAssessor_rankscore | |
| 166 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 | |
| 167 MutationAssessor_score | |
| 168 MutationAssessor functional impact combined score (MAori) | |
| 169 MutationTaster_converted_rankscore | |
| 170 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 | |
| 171 MutationTaster_pred | |
| 172 MutationTaster prediction | |
| 173 MutationTaster_score | |
| 174 MutationTaster p-value (MTori), ranges from 0 to 1 | |
| 175 phastCons46way_placental | |
| 176 phastCons conservation score based on the multiple alignments of 33 placental mammal genomes (including human). The larger the score, the more conserved the site | |
| 177 phastCons46way_placental_rankscore | |
| 178 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 | |
| 179 phastCons46way_primate | |
| 180 phastCons conservation score based on the multiple alignments of 10 primate genomes (including human). The larger the score, the more conserved the site | |
| 181 phastCons46way_primate_rankscore | |
| 182 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 | |
| 183 phastCons100way_vertebrate | |
| 184 phastCons conservation score based on the multiple alignments of 100 vertebrate genomes (including human). The larger the score, the more conserved the site | |
| 185 phastCons100way_vertebrate_rankscore | |
| 186 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 | |
| 187 phyloP46way_placental | |
| 188 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 | |
| 189 phyloP46way_placental_rankscore | |
| 190 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 | |
| 191 phyloP46way_primate | |
| 192 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 | |
| 193 phyloP46way_primate_rankscore | |
| 194 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 | |
| 195 phyloP100way_vertebrate | |
| 196 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 | |
| 197 phyloP100way_vertebrate_rankscore | |
| 198 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 | |
| 199 Polyphen2_HDIV_pred | |
| 200 Polyphen2 prediction based on HumDiv | |
| 201 Polyphen2_HDIV_rankscore | |
| 202 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 | |
| 203 Polyphen2_HDIV_score | |
| 204 Polyphen2 score based on HumDiv, i.e. hdiv_prob. The score ranges from 0 to 1. Multiple entries separated by ";" | |
| 205 Polyphen2_HVAR_pred | |
| 206 Polyphen2 prediction based on HumVar | |
| 207 Polyphen2_HVAR_rankscore | |
| 208 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 | |
| 209 Polyphen2_HVAR_score | |
| 210 Polyphen2 score based on HumVar, i.e. hvar_prob. The score ranges from 0 to 1. Multiple entries separated by ";" | |
| 211 pos(1-coor) | |
| 212 Physical position on the chromosome as to hg19 (1-based coordinate) | |
| 213 RadialSVM_pred | |
| 214 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 | |
| 215 RadialSVM_rankscore | |
| 216 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 | |
| 217 RadialSVM_score | |
| 218 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 | |
| 219 ref | |
| 220 Reference nucleotide allele (as on the + strand) | |
| 221 refcodon | |
| 222 Reference codon | |
| 223 Reliability_index | |
| 224 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 | |
| 225 SIFT_converted_rankscore | |
| 226 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 | |
| 227 SIFT_pred | |
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228 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 | 229 SIFT_score |
| 230 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 ";" | |
| 231 SiPhy_29way_logOdds | |
| 232 SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site | |
| 233 SiPhy_29way_pi | |
| 234 The estimated stationary distribution of A, C, G and T at the site, using SiPhy algorithm based on 29 mammals genomes | |
| 235 SLR_test_statistic | |
| 236 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 | |
| 237 Uniprot_aapos | |
| 238 Amino acid position as to Uniprot. Multiple entries separated by ";" | |
| 239 Uniprot_acc | |
| 240 Uniprot accession number. Multiple entries separated by ";" | |
| 241 Uniprot_id | |
| 242 Uniprot ID number. Multiple entries separated by ";" | |
| 243 UniSNP_ids | |
| 244 rs numbers from UniSNP, which is a cleaned version of dbSNP build 129, in format: rs number1;rs number2;... | |
| 245 | |
| 246 | |
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247 The website for dbNSFP database is https://sites.google.com/site/jpopgen/dbNSFP and there is only annotation for human genome builds. |
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248 |
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249 The procedure for preparing the dbNSFP data for use in SnpSift dbnsfp is in the SnpSift documentation: |
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250 *( It also provides links for dbNSFP databases prebuilt for SnpSift )* |
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251 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP |
| 0 | 252 |
| 253 However, any dbNSFP-like tabular file that be can used with SnpSift dbnsfp if it has:: | |
| 254 | |
| 255 - The first line of the file must be column headers that name the annotations. | |
| 256 - The first 4 columns are required and must be:: | |
| 257 1. chromosome | |
| 258 2. position in chromosome | |
| 259 3. reference base | |
| 260 4. alternate base | |
| 261 | |
| 262 For example: | |
| 263 | |
| 264 :: | |
| 265 | |
| 266 #chr pos(1-coor) ref alt aaref aaalt genename SIFT_score | |
| 267 1 69134 A C E A OR4F5 0.03 | |
| 268 1 69134 A G E G OR4F5 0.09 | |
| 269 1 69134 A T E V OR4F5 0.03 | |
| 270 4 100239319 T A H L ADH1B 0 | |
| 271 4 100239319 T C H R ADH1B 0.15 | |
| 272 4 100239319 T G H P ADH1B 0 | |
| 273 | |
| 274 | |
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275 The galaxy datatypes for dbNSFP can automatically convert the specially formatted tabular file for use by SnpSift dbNSFP: |
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276 1. Upload the tabular file, set the datatype as: **"dbnsfp.tabular"** |
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277 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 | 278 |
| 279 | |
| 280 @EXTERNAL_DOCUMENTATION@ | |
| 281 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP | |
| 282 | |
| 283 @CITATION_SECTION@ | |
| 284 | |
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285 ]]> |
| 0 | 286 </help> |
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287 <expand macro="citations"> |
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288 <citation type="doi">DOI: 10.1002/humu.21517</citation> |
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289 <citation type="doi">DOI: 10.1002/humu.22376</citation> |
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290 <citation type="doi">DOI: 10.1002/humu.22932</citation> |
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291 <citation type="doi">doi: 10.1093/hmg/ddu733</citation> |
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292 <citation type="doi">doi: 10.1093/nar/gku1206</citation> |
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293 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation> |
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294 </expand> |
| 0 | 295 </tool> |